I haven’t posted here much as my supervisor is a bit of a workaholic and its been tough to find time to do everything that needs to be done and engaging in healthy non-work activities. However, I have permission from my supervisor to share something from my work, a set of three simple scripts I wrote. All these scripts run in the UNIX shell.
They’re probably not the most efficient way to do things but, considering I only started to learn any programming last year, I’m rather proud of them. (I’m not counting some basic HTML or fiddling around with the OHRRPGCE plotscripting language which I used to do a few years ago.) You can find them here on Github.
For these to work I already had the correctly formatted protein sequences and gene groupings. The first script “aligningproteinfamilies” went through the list of groups and used T-Coffee to align those proteins. That result came out in Clustal format which I found tricky to work with, so I wrote “reformatclustal” to pull out only the bits that were important to me; the actual sequence and the consensus scoring. In the new format it was easier to look for a perfect alignment, find the position in the line and then extract the amino acid sequence corresponding to that position with “maxconslenresultv2.”
You might recall that, last year, I spoke about some free on-line educational tools I was dabbling with. I now want to recommend that anyone who has some sort of contact with animals, whether through work, having a pet or just eating meat, take the Animal Behaviour and Welfare course offered by The University of Edinburgh. I found it to be very engaging and an excellent introduction into a subject which affects most of us. It’s a welfare approach so sometimes it has its flaws, seeking to maximise welfare when one might rather stop the practice altogether, but it is science-based and doesn’t push a specific view. For example, they mention that cats kept indoors will be safer and have medical care but have welfare concerns about boredom and lack of choice. Stray animals benefit from free choices but have welfare challenges like being attacked by humans. In addition, there is a lot of extra information available. I didn’t have the time to go through it all but aside from the standard lectures there are extra recorded interviews and Google Hangouts as well as links to books and scientific articles which could be of interest.
At the end of last year, I stopped following Pharyngula, which had been one of my original inspirations for blogging, because I no longer considered PZ Myers to be a good model for rational thought. I felt kinda satisfied to now read that Atheist Ireland has (more symbolically than anything else) publicly dissociated from him. Their complaint is largely based on his “hurtful and dehumanising, hateful and violent, unjust and defamatory rhetoric.” It’s hard to fault them there. He always was less polite than many other writers but there are times when that can be justified and other times when it’s extraneous. His usage was mostly belonged to the latter category.
Lastly, a member of Mensa South Africa posted a link to this infographic on the group’s Facebook feed. It lists 439 topics where Bible verses contradict one another. In places it will no doubt be argued that it’s just semantics and interpretation but others are clear-cut contradictions. For example, regarding the death of Judas, Matthew 27:5 says:
So Judas threw the money into the temple and left. Then he went away and hanged himself.
While Acts 1:18 says:
With the payment he received for his wickedness, Judas bought a field; there he fell headlong, his body burst open and all his intestines spilled out.
For those that don’t know, Steam is Valve Corporation’s digital distribution software that’s used for buying, managing and playing games online. If you want to play any modern games these days (at least legal copies), it’s pretty much essential software. However, the customer service and support is almost completely non-existent.
Take this scenario. You get given a present but the item is incorrect; perhaps it’s a book that you’ve already got or maybe it’s a PS4 version of a game when you have an X-Box. You go back to the shop where it was bought, explain the situation and exchange it for something else or the correct version. Some shops might require a receipt but you’d struggle to find one that wouldn’t be happy to do the exchange and keep a customer happy. Continue reading
There’s an interesting story about crows from the BBC (found via io9) about a girl who regularly feeds crows. That wouldn’t be so remarkable if the crows weren’t now giving her gifts in return. We probably shouldn’t be too surprised. Crows are highly intelligent and have long term memory of people. There are wild animals that can think and feel and reciprocate a person’s gifts. If people had more interactions with animals we would probably hear more such stories. At the moment they tend to be limited to pets.
One of my recent quicklink posts (well… December) mentioned both the need to reduce consumption of meat to reduce (drastically) our impact on climate change and the strong opposition that meets such proposals. In a heartening, though non-binding, move, the Dietary Guidelines Advisory Committee have released their 2015 scientific report to the US Department of Agriculture and Department of Health and Human Services which explicitly mention reducing consumption of meat due to the effect on climate change. This is covered in Slate.
In the world of computing it seems like we are gradually winning the fight against unnecessary and invasive internet surveillance. Not necessarily because everyone has been convinced but because the people fighting surveillance are a cohesive movement. And then there’s also an interesting piece on how discussion about security vulnerabilities in code can be prevented laws. The main feeling of the article is frustration at how laws prevent important ethical discussions.
Free speech is absolutely vital for the sort of society in which I wish to live. I want a society where ideas can be freely exchanged, where they are judged on their merits alone and not on who supports or derides them. If we do not have freedom of speech then there can not even be debate on any other issue. This is something I’ve tried to defend throughout the history of this blog, whether it was calling out France for outlawing opinions, the UK for arresting people for harmlessly expressing their views or just arguing against offence being something we should be protected from. Now I need to do it again. Continue reading
Science reporting can be tricky but if your job is to report on such topics then you should do it responsibly. A recent article on Yahoo!, written by Elise Solé, shows a number of bad reporting habits that should be discouraged, starting with the sensationalist headline.
Why Teen Girls Should Avoid Soda
Drinking sugary drinks is bad for you and everyone should try to cut down. I essentially stopped drinking sugary drinks a few years ago for the sake of my teeth but there are many benefits to cutting them completely or merely reducing consumption. However, that’s not what this article is about. Compare it to a headline from another news article on the same subject (I’ll tell you why I chose this one later). Continue reading
It’s been a long time since I’ve posted but that’s been due a particular busy time with me returning to Vienna, needing to find a place to live, starting the PhD course and, with terrible timing, falling sick. All that has left little time or energy to blog but I’ve had a breather today and will toss out a couple of links.
One of the biggest stories while I’ve been inactive was the Charlie Hebdo attack and later supermarket hostage drama. To do something different I’ve decided to post two links about positive Muslim activities regarding the attacks. Malian Muslim Lassana Bathily, who worked at the Jewish supermarket that was attacked, hid six people in the freezers during the hostage situation as well as escaping the building to inform police what was happening inside. Last I heard there was talk of awarding him French citizenship for his bravery. On imgur there is a collection of heartening cartoons from Arab newspapers expressing support for Charlie Hebdo.
In less heartening news there is an example of sexism from a Jewish newspaper that Photoshopped all the women out of a Charlie Hebdo rally photo. In Ireland we have the simultaneously depressing and funny “Sounds of Sodomy” sitation.
And, just so we don’t end on a low note, here is a collection of animals that are benefiting from prosthetics.