Archive for January, 2014

Open wide, let me put this in you

Thu Jan 30, 2014 12:52 am by Prolescum

Given that the UK Government is considering switching to open source formats and software, and that several municipalities (or entire government departments) within and without the EU have decided to ditch proprietary software in favour of FOSS (Free and Open Source Software) alternatives, it’s worth us having a look at the pros and cons of such a move, if only to better understand (or object to) the decisions being made at this level.

Firstly, a quick explanation of the terms are in order:

Open Source Software: See here for the official Open source Definition

Open source is a development model based upon the “four software freedoms” elucidated by Richard Stallman of the Free Software Foundation as: the freedom to run [the] software for any purpose; the freedom to study how the program works and change it to suit your needs; the freedom to redistribute the code; the freedom to distribute your modified software so others may benefit from your changes.
The free in Free Software refers to liberty, not price. In practice, this means that using software with an open source license gives developers, engineers and end-users the ability to share their ideas and make contributions (fix errors or bugs, add new features etc) that benefit anybody using said software. It also means that the code is available for constant review, giving rise to the argument that FOSS deals easily and promptly with, for example, security issues.

Proprietary Software:

Software licensed under the exclusive terms supplied by the copyright holder. Generally speaking, proprietary licenses give the right only to use the software under certain conditions, in practice meaning that one is restricted from modifying, sharing, studying, distributing or reverse engineering the code.
Only the provider of the software has access to the source code, and therefore only they can modify, release updates or add new functionality to the software.


It’s worth noting that both proprietary and open source (or free) licensing uses the same legal basis (usually copyrights) to construct agreements. Proprietary licensing (most often in the form of an End User License Agreement) will state precisely what you can and cannot do with your purchased license, whereas open source licenses can vary from completely free, i.e. no restrictions at all, to the requirement that published code must be released using the same or equivalent licensing.

So how would it benefit government departments?

1. Switching formats (for example from Microsoft’s proprietary .doc Word document format to the open standard .odt format) could mean that all government departments regardless of operating system or software in use will be able to read and write to the same target and expect the same results. Of course, I suspect this happens now with office documents, but is burdened by an EULA with an annual fee.
As the format has new features added, no additional cost is applied outside the manpower required to roll out the updates. This would also make it easier for the various departments to deploy a variety of operating systems depending on their needs without the burden of having to re-format documents for particular users.

2. Overall costs of deployment are reduced (not paying for licenses or new iterations of the software, for example). This is a disputed one, as a counter argument exists. The cost of retraining staff for using new software, and the cost of training or employment of new IT staff with a new system has been said to vacuum up any savings made by switching.
As it currently stands, much of the UK Government is still using versions of Windows and other related software created well over a decade ago, so I believe the retraining costs of switching would amount to much the same were they to update to more modern versions, with the added benefit of lower future spending.

3. Updates, bug fixes, plugins and tweaks etc can be created in-house without additional licensing or approval. Most IT departments, whether government or business, have employees who write and deploy software for front- or back-end offices. An easily understood example might be an intranet where employees have access to FAQs, forums, customer databases and the like. As has been my experience, certain parts of an intranet may make use of bespoke Internet Explorer (Microsoft’s default browser) features, such as ActiveX plugins. Only IE supports ActiveX, and only Microsoft decides whether a plugin is still useful or will be deprecated.
This is a problem because the choices are often either to use an outdated browser (not secure when used outside the intranet) or rewrite from scratch to whichever iteration they update to. This is a vicious circle, and would be ameliorated by using an open standard such as HTML5 to code the intranet and open source software to maintain legacy features (for example by using a browser’s plugin architecture or altering its code) while keeping up-to-date with regards to general internet security.

4. Writing your own software. Libraries and back-end services written for one open source program can often be used in other programs without express permission (depending on the license), lessening the burden of writing new ones from scratch.

What are the downsides to switching?

1. With regards to format-switching, Microsoft Office now supports open document formats, so only some brief training informing staff to save in .odt would be required. Switching entire platforms may require further training due to the variety of options available outside the proprietary software pool, however, given that various departments may be required to give training for new versions of proprietary OS deployments, I believe the costs are comparable.

2. Long term viability. An issue that comes up within the Open Source communities is what to do with a project when its creators or maintainers decide to no longer support the software. This could add to the overall costs if a department depends on some code that is no longer supported, as it may require a switch to an alternative or for the IT chaps to maintain it themselves.

3. Interoperability. An issue that plagues the modern world as a whole, really, but one that should concern a government considering deployment of FOSS. An example might be using Microsoft’s Exchange for email. Support for ActiveSync et al outside the Windows environment is choppy, if not appalling.

4. Regulations. There may be legal requirements upon software deployment, such as using particular encryption methods or in fact using software with specific licensing restrictions, exemptions, or requirements. I believe this would be the issue most necessary to adhere to, and the most difficult to overcome.

All cards on the table, I am an advocate of FOSS, so my opinions should be regarded accordingly.

That said, these are only a few of the pros and cons we should consider (the ones that came to mind when writing this post…). Can you think of any other issues governments could run into from a switch? Or perhaps you’ve noticed a benefit not noted above? How about a mistake I’ve made? Comments and suggestions very welcome through the comments link below.

Further reading:

List of Open Source Licenses
Legal Issues and Best Practices around procuring or deploying open source software

Science writing: Tools

Tue Jan 14, 2014 12:24 am by Inferno

I’ve not given up on my other posts, I’m just not in the mood for them at the moment. Politics is generally pissing me off because we have such a shitty government and I don’t want to write about schools at the moment, just because. 😉

OK, now on to what’s currently happening. I’m in the middle of writing a paper for a journal, I’m writing a mock-paper for a seminar and I’m writing my Bachelor’s Thesis. Naturally, my mind is preoccupied with academic writing.

I’ve found a few wonderful papers on how to read a paper (Inception, isn’t it?) and I will try to put a list together soon. (So anywhere between 6 and 12 years.) For the moment however, I want to focus on a few tools I use to organize my papers, find sources, put everything together and just generally make my academic life easier.


First up, my computer. I own a crappy, 4-year old laptop. It’s loud, it’s slow and dang, does it heat up. So for those times I want to read/write in my bed, I bought a cooling pad. You can have them for 5$ a piece, I bought mine in Sweden and it’s of slightly superior quality so I had to put down 30$.

The laptop itself has 4Gig Ram, 2.1GH and a Radeon HD 5145. That means I can use most graphics programs out there, including Adobe Photoshop and Video programs. I don’t need those, but I do occasionally put together pictures/graphics, for that I use photoshop.

Another thing you absolutely need is an external hard drive. I got my 500GB (more than enough for working purposes) for a little under 80$ and that was ages ago. You can now get 1TB for the same price. (Don’t forget the 1. If you just get TB, that’s money badly spent!) On that HDD, you want to store your papers and make backups of your computer. I’ve had a colleague in who lost his BA’s Thesis and damn, was he fucked.

Also essential: A few (2-3 minimum) USB-drives. I’ve got one with 2GB, 4GB and 8GB each, plus a few others. One of them is a second backup for my library, the others I use for current writing. Also essential: Create a dropbox or mediafire account and upload your work. My complete library of papers, books and University-related stuff currently runs at just over 2GB, plus another 1GB of video-lectures. Mediafire gives you 50GB, Dropbox 5GB, so that’ll easily fit.


Now that you’ve got the potential of storing your files, you need some stuff to organize them, find files and write them.

Most importantly: A browser.
I personally use Chrome, but have used Firefox before. Both are good, depending on what you need. I prefer Chrome because of the layout and usability, but again I wouldn’t mind using Firefox. I haven’t used Mobile, I would discourage you from using Safari and IE and I’d probably not use Opera, though I have in the past.


So assuming you’re running Chrome, I’ll run you through my extensions. Because I’m a cruel computer user and leave about 10-15 tabs open at any given time, I use Xmarks to synchronize my tabs and bookmarks. If ever I lose them or my browser crashes and Chrome’s inbuilt safe-system fails, I just click on Xmarks and re-open my tabs. Handy, but not essential.

Next up, Lazarus Form Recovery. Have you ever written a perfect post, your browser died and your post was gone? Well, Lazarus has (so far) saved me from re-writing about 10k words. That’s quite a bit.

I’ve already written about Unsourced and Rebutr before, so I’m not going to repeat myself. Problematic: I’m not using them any more, they’re just not updated quickly enough.

Now for the jewels in my collection. First up, I own a Kindle as of last week. It’s not only 40$ and it really makes your life easier, so don’t be a snob, buy one. Install sendtoKindle and it will give you an excellent little extension on your browser. You see a document you might want to read, you click on the extension and send it to your Kindle. The size is adapted so you can easily read it and the format is great. With this extension, I’ve already sent about 20 science-y articles to my Kindle, so now I can ride the metro and catch up on my reading. (My only problem: PDFs are huge! My Kindle should be able to fit 1400 books, but after about 50 PDFs it’s about halfway full.)

The second extension may be even better: Evernote Web Clipper, in addition to the Desktop-version of Evernote. With it, you can save articles (or pictures) from the web. Just search them in your browser, click the extension and save the article, save it as a PDF, take a screenshot… etc. In the desktop-version, they synchronize automatically, you can then organize them using folders or tags, depending on what you like. It saves the URL, you can read the complete article (depending on how you saved it without comments (eg. blogs) and without ads) and you can write in the article. Holy shit this thing is awesome! You can also export them as PDFs (for use on your Kindle) and you can sync it with your smartphone.
Obviously you can also use it the way it was intended to: As a digital scrap book.
Additionally, you can network with people. I’m currently exchanging information with my Professors at University. Any article they deem worthy of my interest, they send me with one click. And vice versa. Networking bitches, it’s fun!


Furthermore, I run a few programs on my computer that are not attached to my browser. I’ve got the usual anti-spyware/anti-virus software (AVG in my case), I’ve got some pc-performance programs (DLL-Files Fixer at 15$ and TuneUp Utilities 2014 for 25$) and a few programs for keeping in touch. (E-Mail organizers for my 3 different E-Mail accounts, Skype, Teamspeak, etc.)

One of the programs I use is Light Image Resizer. Sometimes I need to send in a JPG in a different format, make it smaller, make it bigger, etc. I’m sure there are better programs out there but this one does the trick for me.

I use Audacity to analyse any interviews I did and I use Pamela to record Skype calls.


And now come the great heroes of my desktop. I am now going to reward you for reading through this post.

One of my most important and most used tools: Clipmate. Anything you Ctrl+C, you can find again in Clipmate. You can also take screenshots of exactly the area you want, no fudging around with Windows screenshot and then manipulating it in paint.

My newest addition and already one of my most important ones: Mendeley. It has three main uses:

1) Organizing a library of any papers you have digitally stored. I download masses of papers as PDF files and they all get weird names when you DL them. For example, I downloaded an article from the journal “Advances in Teacher Education” and got a PDF called “01626620%2E2013%2E846148″. That’s not really helpful if you’re trying to find it on your PC. You could of course rename it to “Author (Year) Paper Name” but let’s be honest, you’re not. With the roughly 600 papers I have on my PC, it’d take me a month just to get through them.

So what do you do? You drag them into Mendeley and hey, presto! all your articles (well, most, some bugs apply) are organized by Author/Year/Paper name/etc. All relevant info is extracted and now you can easily browse them.

2) Finding papers. On the Mendeley website, you’re able to browse citations, take a look at what your colleagues are browsing and so on. Searching for the most popular article in earth science? Click! Searching for most viewed article last month? Click. Really easy.

3) Networking. There are loads of groups, thousands of people are using Mendeley, most of them researchers. Add contacts, add groups, share documents.

Finally, my two smaller programs. I use PDF Architect and PDF Creator in tandem. Both have their down- and upsides. You just need some kind of PDF manipulating program.

Also, I don’t present on PPT any more, I only use Prezi. Interestingly, not many people know about it so they’ll be totally freaked by your rotating presentations. Just make sure you don’t make it too flashy, otherwise content gets lost.


So there, those are my programs and extensions. I use a few other programs for my teacher-related work (like HotPotatoes to create worksheets), but those are my main working programs. If you’ve got any other splendid programs/extensions for making life easier, do share them. Also, I’m getting my first smartphone in the summer (yes, I still have a phone that doesn’t have a camera), so I’d also be glad if people shared apps. I know of only two: Macmillan’s phonetic transcription app and’s downloadable dictionary. (Satisfactory for classroom work, but not for anything else.)

Philosophy for life

Fri Jan 10, 2014 11:56 am by Aught3

In his book modernising the ancient Greek philosophy of Stoicism (A Guide to the Good Life: The Ancient Art of Stoic Joy), William Irvine proposes two criteria for a coherent philosophy of life. The first is to have an ultimate goal in living. Of the things that can be pursued in life, the ultimate goal is the one you find most valuable. It is a grand goal that sits at the top of a hierarchy and is something you would be unwilling to sacrifice in the pursuit of other ends. Without an ultimate goal, a philosophy of life is incoherent.

According to Irvine, the second component in a coherent philosophy of life is a strategy for achieving your ultimate goal. The strategy tells you how to go about your daily routine in a way that enhances your ability to achieve the thing in life that you define as the most valuable. Without an effective strategy you will likely fail to achieve your grand goal and so a coherent philosophy of life needs both an ultimate goal and the means to achieve it.

Everybody has a philosophy of life, it’s just that most people don’t think about it. For such an important topic, philosophy of life isn’t discussed at school, universities don’t offer courses, and treatment of these topics in popular culture is next to zero. Without proper consideration of this issue, the life philosophy foisted upon most people is enlightened hedonism. The ultimate goal in hedonism is pleasure and the ‘enlightened’ part refers to the strategy. An enlightened hedonist takes time to consider which pleasures they will pursue, at what time they would like to enjoy those pleasures, and the best method for obtaining them. Another thoughtless source of a semi-coherent life philosophy is an inherited religion. In a typical religion the goal is to obtain a good second life and the rules and precepts lay down the way to achieve that goal. Since everybody has a life philosophy the only difference between people is whether they have thought about their ultimate life goal or have just accepted it.

The biggest danger with having the wrong life philosophy is the chance that you will mislive. Despite all the things you did at the end of your life you will look back only to realise you did not live it the way you wanted to. Either you chased the wrong goal or, if you had the correct goal identified, you were unable to live up to it. As Irvine puts it “Instead of spending your life pursuing something genuinely valuable, you squandered it because you allowed yourself to be distracted by the various baubles life has to offer.” An enlightened hedonist may realise the pursued pleasures did not really bring what was most desired and the religionist may come to the understanding that their strategy will not bring eternal life after all. Without a suitable philosophy of life you will waste the one and only life you know you are going to get.

Some alternative answers to the philosophy of life question are: virtue, tranquility, happiness, connection, service, exploration, and usefulness. My suggestion to you is to find your own answer to the question “what do I want out of life?” Ultimately, your grand goal in living is the most important thing for you to discover. Understanding it will change your life – for the better.

Know Your Bones: January 2014

Mon Jan 06, 2014 10:26 pm by he_who_is_nobody

Last month’s challenge was very easy. It was so easy that duclicsic posted a correct answer within minutes of the blog going up. However, later in the month Aught3 posted an even more correct answer:


Dimetrodon limbatus

Reason: Google-fu


This is a specimen of Dimetrodon and Aught3 is even more correct in that it is specifically Dimetrodon limbatus.


 (Taken at the New Mexico Museum of Natural History and Science)

Dimetrodons inhabited the earth 295 – 272 million years ago, during the Permian. Dimetrodons were most likely the top predator on earth during that time. The most prominent feature of Dimetrodon is the sail on its back. The sail was most likely used as a heat regulator, but some scientists have suggested that it might be an example of sexual selection, similar to the Peacock’s tail. Either way, the sail on its back and four-legged posture makes Dimetrodon one of the easiest prehistoric critters to identify.


There is confusion about Dimetrodon, in that several people believe that it was a dinosaur, I think this is because Dimetrodons are always found in Prehistoric Play Sets and most people believe dinosaurs were just big lizards. Dimetrodon does resemble a large lizard with a sail on its back. However, there are three main reasons Dimetrodon was not a dinosaur; the first most obvious one is that it is much older than any dinosaur. The second is the sprawling, lizard-like stance of its legs. Dinosaurs’ legs, unlike lizards, are directly under their bodies and not protruding from the side of the body like modern lizards. The third is that Dimetrodon is actually more closely related to modern mammals than it is to reptiles such as dinosaurs.


Dimetrodon belongs to the synapsid clade along with all mammals. This means that behind the eye, there is only one hole for muscle attachments. Dinosaurs belong to the diapsid clade, meaning they have two holes behind the eye for muscle attachments.


Moving on to this months challenge:


 (Taken at the Dinosaur Museum and Natural Science Laboratory)

Good luck and happy 2014.

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