Yesterday’s excellent Australian Pathogen Bioinformatics Symposium 2014 (#APBS2014) reminded me that this post was a bit overdue: originally posted at the UNSW Science Wavelength blog on October 30, 2014. Following APBS2014, we are also looking into how we can identify which other pathogens might be using a similar strategy.
Read more at the Edwards Lab blog…
If there’s one thing that irks me as much as Homeopathy, it’s the anti-vaccination crowd. Therefore, I think that posts like the recent “Dear parents, you are being lied to” at Violent metaphors, deserve as much publicity as they can get. It's a well structured piece, heavily laden with links for further reading, with a heartfelt plea:
In only one respect is my message the same as the anti-vaccine activists: Educate yourself. But while they mean “Read all these websites that support our position”, I suggest you should learn what the scientific community says. Learn how the immune system works. Go read about the history of disease before vaccines, and talk to older people who grew up when polio, measles, and other diseases couldn’t be prevented. Go read about how vaccines are developed, and how they work…
As Professor Simon Foote wrote around a year ago, Parents have a moral obligation to children. Make no mistake about it, failing to vaccinate puts both your children and the children of others at risk. (And not just children.) As the Jenny McCarthy body count reports, preventable deaths in the US alone have exceeded 1300 since 2007, with 100 times that number of preventable illnesses. Whilst not the sole cause, anti-vaxxers must take a share of the responsibility for this.
Like Jennifer Raff at Violent metaphors, I’m sure that some of those opposing vaccination and/or advocating “parental choice” are doing so with the best of intentions. However, good intentions are no defence against disease and anti-vaxxers across the spectrum should take a long, hard look at themselves and ask whether their reasons for opposing the overwhelming global medical and scientific consensus are worth endangering even one life.
If you're not sure, I highly recommend reading the whole article. And if that’s too tame for your tastes, there is also the classic “Angry scientist finds an uneducated internet comment and delivers an epic response…”, which has a slightly less nuanced (but also informative) correction of some anti-vaxxer lies.
It’s still (just) Darwin Day in some places but I must confess that it came upon me too fast this year. Still, it’s a good excuse to revisit some of the previous Darwin posts about Darwin and Wallace, Darwin the gentleman scientist and last year's Darwin quotes for Darwin Day.
Better still, check out some Darwin Day posts from elsewhere: How Darwin took on Intelligent Design at the Rationalist Association, or a suite of posts at Why Evolution is True, including Darwin’s pet tortoise!
Every now and then, something comes along that just needs to be re-blogged. I give you, The fabulous pom-pom crab!:
h/t: @JohnRHutchinson via WEIT. (Original source unknown.)
Before we sold our old house and moved to Australia, my wife commissioned a unique souvenir and a beautiful surprise present for me: a line drawing of our old house by John Roued-Cunliffe. Using a photograph plus some artistic license to place our two cats, Mia and Arthur, on the scene, John rendered a lovely keepsake:
John’s wife, Eddie, is friends with mine and she also has a blog, which features one of John’s illustrations. I think it’s great! Christmas is coming up, so if you’re stuck for present ideas then check John’s website!
For more on Darwin and Wallace, have a read of today’s guest post on Why Evolution is True by Greg Mayer, Darwin and Wallace at Burlington House. With extensive references and direct quotes from Wallace himself, it makes an interesting read.
The accusations against Darwin are that he ‘stole’ one or more ideas from Wallace, and that the circumstances of the reading and publication of the Linnean Society papers were somehow unethical. Although ostensibly arguing on Wallace’s behalf, these authors must dismiss Wallace’s own accounts (e.g. 1870, 1889, 1905, 1908) of the contributions made by Darwin and himself, and paint Wallace as a victim. But, as his biographer Raby (2001:291) says, “Wallace was not a victim, and he did not see himself as a victim”; to do so “diminishes both Darwin and Wallace.”
Hopefully the conspiracy theorists will now stop diminishing both of these great Victorian scientists and celebrate them both.
I often set up draft posts by emailing pictures to my blog to add text etc. later. If, like me, you sometimes email multiple images from an iOS device and wonder what happens to the resolution if you resize it to Small/Medium/Large. Happily, a post at Senseful Solutions on iPhone Email Image Sizes has the answers, some of which are summarised below:
| Size | Picture (JPG) | Screenshot (PNG) |
|---|---|---|
| Small | 320 x 239 | 213 x 320 |
| Medium | 640 x 478 | 426 x 640 |
| Large | 1296 x 968 | |
| Actual | 2592 x 1936 | 640 x 960 |
iPad screenshots are 768 x 1024 PNG files.
My last post was number 400, which has caused me have a reflective moment about my blogging. (And the 87 drafts in various states of incompleteness!) One of my New Year’s aspirations was to blog more original science papers. Half a year on, I’ve not really done that well, to be honest. (Nor on my other aspirations, to be honest: Mystic Mog and the Exploding Tortoise has been on hold since Jaunary!)
Part of the reason is the impending move to Australia and all the organisation and house-selling that goes with it. A bigger part of the reason, though, is that (for me, at least) science blogging is hard! I have a lot of respect for those who can do it well, like Jacquelyn Gill and her ecology & climate change blog, The Contemplative Mammoth. (Her most recent post, The many scales of climate change, part 1: Tectonic timescales is well worth a read and I am looking forward to the parts to come.)
I consider science communication to be an important part of my job and I really want to get better at it. Happily, it is not too late. We are about half-way through 2013 and so there are 25(ish) weeks left. The only way to improve is to practice and rather than risk upsetting anyone by getting their science wrong, I have therefore decided to aim to blog one of my own papers each week to see how that goes. It may not happen but by making a public declaration of sorts, I am hoping I will get the extra motivation boost needed to make it happen. (Embracing Markdown should help too!)
In a recent post, I extolled the virtues of Markdown as well as the online Markable editor and the Markdown Service Tools available for Markdown to HTML conversion in Mac OSX. This got me to thinking whether I could use Markdown to speed up writing some of my blog posts.
For ease of controlling the layout and context - and potentially re-using text and HTML - I write all my blog posts in the Blogger HTML window rather than using the “Compose” tools. I’m not entirely sure why but I just tend to prefer the result. (Part of it, I think, is the purity of the underlying HTML - what that says about me, I’m not sure I want to know!)
I often email myself content and plain text notes to tidy up later (hence the massive pile of half-written draft posts that I have) but since (re)discovering Markdown, I have started making more notes in Markdown and wondered if I could harness that in my blog writing. Blogger does not have a dirext Markdown editor, sadly, but there does seem to be a pretty convenient solution for Mac users, at least.
1. Install Markdown Service Tools. Brett Terpstra’s Markdown Service Tools offer, among other things, the capability to direct copy Markdown onto the clipboard as HTML code or make the Markdown to HTML conversion in place.
2. Write your Markdown in Markable. Whilst not strictly necessary, writing the Markdown in the Markable editor will catch any problems with your Markdown as you go.
3. Convert your Markdown to HTML. Windows users might need to export the HTML and then open the file in a text editor to copy and paste into Blogger. On a Mac, with the Markdown Service Tool, it is a bit easier - although, sadly, not quite as easy as I had hoped. The Service to use is:
md - Convert - HTML to Clipboard
Unfortunately, this does not seem to be available for highlighted text in the Markable window. Instead, there is the need to first copy and paste the text to a regular text window. This is not so bad, as the regular Blogger window itself will do. You then need to use the conversion service and paste back into the Window. Alternatively, just use:
md - Convert - MultiMarkdown to HTML
This will convert the text in place. You can either use the Services menu item (or right-click), or you can setup a Markdown Service Shortcut to do it all with the keyboard.
4. Make sure that line breaks are used. One thing I noticed when converting the HTML is that it (sensibly) uses paragraph markers. If, like me, you use Blogger’s capacity to Press “Enter” for line breaks, you will need to change this. (The laziness and readibility this option enables are not needed when using Markdown anyway.)
5. Add pictures, tidy and post. With the main text, links and formatting in place, it is now a simple case of adding the pictures, tags etc., giving the post a quick preview (and tidy if necessary) and unleash it to the world. The added benefit, of course, is that you have an extra copy of your post saved in Markable in case anything goes wrong.
As well as the line endings issue, there are a few disadvantages of doing things this way. One problem is that if you Preview a post and then spot an error, you have three obvious choices, none of which appeals:
The latter is obviously the best if the changes are large but what if you have already added extra pictures and things?
One solution is to convert your HTML back to Markdown to continue editing.
md - Convert - HTML to Markdown
This has pros and cons. One pro and con is that the new Markdown does not necessarily look like the original. This can teach you new Markdown but might also confuse!
The picture placement and formatting also does not remain quite the same and may need re-jigging once the Markdown to HTML conversion is repeated. This only seems to be a problem for left/right-aligned images, though. It's also a fairly easy way to get images into Markable files, if that is your goal!
It may not be suitable for every post, and there is a good chance I will end up going for tweaking option 1 (abandoning the Markable version) in most cases, but it could prove a useful way to write posts with a lot of links and formatting. If nothing else, it's another good way to develop some Markdown skills.
I'll always have a bit of a soft spot for the journal "Molecular Biology and Evolution" (MBE). Not only does it combine two of my favourite things - molecular biology and evolution - but it was also where I published the main paper from my PhD, Transiently beneficial insertions could maintain mobile DNA sequences in variable environments. Although published by Oxford Journals, MBE is a journal of the Society for Molecular Biology & Evolution (SMBE), which also organises a large annual conference of the same name. 
The Rationalist Association has a new website at http://rationalist.org.uk/, which is packed full of articles and podcasts etc. Many of these are from the excellent New Humanist magazine. The site is still under development but the goal is to establish a vibrant online community and so they are currently offering a free opportunity to become a Founder Member and help shape its future. If you are into promoting reason, debate and free thought, why not sign up? I have!
"A favourite and fashionable argument for God is the argument from a fine-tuned universe. The argument is that, were it not for many aspects of our universe being “just right” for us to exist, then we wouldn’t be here, therefore [and that "therefore" is the big leap] the universe must have been fine-tuned to produce us."His response is devastating and draws attention to six major flaws in that argument.I've touched on bits of this before (although with considerable less eloquence) but I recommend reading the coelsblog post for the full six. (It's not that long.) Coel's 3b is my new favourite, though:
"The occurrence of things for which their environment was NOT “just right” would be a far better indicator of intelligent intervention. For example, an animal in a zoo is indicative of intelligent intervention; an animal that fits perfectly into its ecological niche is not an indication of intelligent design, but instead is amply explained by non-intelligent processes such as evolution. Thus, if we found ourselves in a universe that was not suited to creating us then that would be far better evidence for intelligent intervention!"As he points out in another great post from Jan 2, Science can indeed answer “why” questions, it's not "that science cannot give answers involving gods", it's just "that science does not give such answers". Science also remains open to the possibility that, ultimately, there is no "why" at all. It is not that science has decided up-front that there are no gods, it is just that it currently has "no need for that hypothesis". Many atheists, myself included, are the same.
I was hoping to do a bit of an End of Year review for the blog with the top posts of 2012. Unfortunately, blogger does not seem to be able to provide annual stats - it's limited to the last day, week, month or all time. Google Analytics is more useful but, unfortunately, I only set it up on the blog in April so I cannot use that either. Instead, here are the top six posts from 2012 based on all time stats at the beginning of January:| # | Post | Date | Views |
|---|---|---|---|
| 1 | Kumala Zenith Merlot/Cab Sav/Shiraz - another bargain red | 6 Feb 2012 | 381 |
| 2 | There's nothing scary about the Spice Kittens | 16 Oct 2012 | 360 |
| 3 | Tim Minchin talks to Caitlin Moran | 30 Aug 2012 | 273 |
| 4 | How to root a phylogenetic tree | 7 Jun 2012 | 183 |
| 5 | A fan fixes Star Wars (Machete Order) | 7 Oct 2012 | 181 |
| 6 | Finding Nemo's sex-changing father | 18 May 2012 | 159 |
I'm not a great believer in New Year's Resolutions. After all, if there's something you should change in your life, do it when you realise it, don't wait until the end of the year. There is also the potential issue of self-recrimination etc. if you fail to keep them.
☑ Make more time for writing. I've got a few papers and a book chapter that need writing. Episodes of Mystic Mog and the Exploding Tortoise have also been decreasing in frequency down to a disappointing 4 in December. There are a number of contributing factors to this but one is clearly not setting aside time to write.
My recent revisiting of the iPad BlogPress App has made me curious about the Blogger App for the iPhone. Like BlogPress, I have not used this for a long time - I may have abandoned it when I first discovered BlogPress - but also not deleted it. I therefore thought I'd try a quick post with it to see how it works.
This morning, whilst feeding the cats, I came across the very fun - and educational - OneZoom Tree of Life Explorer, described in a PLoS Blog article, Fractaltastic Evolution. Currently, it only has mammals and amphibians but it will grow. Birds are next and plans are afoot to use Open Tree of Life data to extend it to 2 million species (or maybe more by then).
One such project that caught my eye a while ago was ProjectEvoMap - A global map of evolutionary biology research groups, started by an English PhD student in Sweden, Robert Griffin (#ProjectEvoMap). I'm not 100% sold on the name - if, like me, you try to find it and insert a space after "Project" you get all sorts of other stuff - but I really like the idea. It's a pretty simple aspiration: to enable people to locate evolutionary biology labs near places of interest and to generally raise awareness of what (and where) evolutionary biology is being done. I've added my lab and if you're an evolutionary biologist reading this, I hope you'll add yours too.
