Archive September 2010

Anniversary day for Code for life Grant Jacobs Sep 30


It’s year since my first article on this blog. Happy blogoversary to me!

Although I wrote a couple of guest posts at Alison’s bioBlog before starting Code for life, and recycled my ‘About’ page as an introductory post on September 24th, my first article, Scientists can’t write?, was written on September 30th, 2009. (I also published just two articles online in 2002 in an aborted bioinformatics/science column.)

I’ve posted 360 articles (excluding this one) and received 1790 comments. (Bear in mind I often use comments to add follow-up information.) I’ve received whole lot more spam – over 63,000 spam comments and counting…!

I’m allowed to indulge myself for one day, I think. Below are some I have gathered (far too many) picks from my first year of blogging. This list is really for my own use but you’re getting the benefit. Or misery depending on your point of view. Well, you don’t have to read them: you can ignore them…

These aren’t necessarily the ’best’ of what I’ve written, nor the articles that have attracted the most comments (which tend to be health-related issues that got over-taken by advocates). They’re just ones that appeal to me.


Science communication


I’ve written several posts head-butting various natural health lunacies over the year. I’ve opted to skip most of them here. They’d make this collection grumpy and beside they feel repetitive to me as the people promoting these ’cures’ make the same errors repeatedly…

Bioinformatics and computational biology


Practicing science

Trivia and fun

I’ve presented a lot of these, but have left most aside as these most often highlight someone else’s content (esp. videos) rather me bringing much to them.

Any Brits abroad here? Grant Jacobs Sep 29



I hope by now that British scientists abroad are aware of the Science is Vital campaign in response to noises from politicians to cut science spending in the UK.* If you aren’t, head over to Jennifer Rohn’s In which I call my own bluff and familiarise yourself with the details. You’ll want to sign their petition. At the time of writing, there are in excess of 5,800 signatories. A march is being organised in London.

* I don’t have a good handle on the scale of the cuts, but figures of 10-20% are being bandied about. If so, these would have a major impact.

Other articles on this topic:

(I’ve two minds about posting this: this is very late in game so it makes me look tardy – to say the least – but then I’d hate to see anyone who cared about the issue miss out.)

Choosing an algorithm – benchmarking bioinformatics Grant Jacobs Sep 28


You’ve been asked to to run a bioinformatics analysis. How do you choose what algorithm to use?

My first suggestion would be to talk to experienced bioinformatics scientists or computational biologists. It’s a lot quicker, and it’ll save you making mistakes that the research literature assumes you know better not to. You’ll also avoid the trap of thinking that something is simple that in fact isn’t. In particular, you should talk to your local analytical experts well before collecting the data, ideally before drafting the grant application.

Structural alignment of thioredoxin (Source: Wikimedia Commons)

Structural alignment of thioredoxin (Source: Wikimedia Commons)

Putting that aside, let’s look at the case of you choosing an algorithm yourself. (Perhaps you are the local bioinformatics support person or you are a biologist with one fairly simple, specific thing to do.)

For most common tasks, there are several possible algorithms you could use. Which one is best for your specific problem?

The first thing you need to do is to define the biological problem you want the analysis to resolve accurately. Aside from ensuring that you are actually trying to solve a specific problem and not ’just doing something’, you can’t possibly make an informed decision on what algorithm to use without this. (Don’t laugh at the first point, I’ve seen plenty of ’bioinformatics’ figures in lesser papers that seem to just be filling space.)

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Pick the Nobel winners and win Grant Jacobs Sep 28

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Are you a hard-up Ph.D. student or post-doc looking for a chance to win a freebie? Or a staff member looking for a present for the kid on the cheap?

MedGadget are running an on-line competition: enter in the comments your predictions of who will win the Nobel prizes, being announced from next week, and your name goes in for an iPod. (An iPod Nano for each single category predicted correctly, and an 8Gb iPod Touch for predicting all three science prizes correctly.) Those outside the USA, Canada or the EU win cash.

If you don’t like entering this, but want to share your punts anyway, there’s always the comments below.

(H/T PZ Myers. If you know of any other competitions, let us know in the comments.)

Where do good ideas come from? Grant Jacobs Sep 27

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One of my favourite quotes is:

The most exciting phrase to hear in science, the one that heralds new discoveries, is not Eureka! (I found it!) but rather, ’hmm…. that’s funny….’

(Isaac Asimov)

Good ideas are often not from sudden understanding but from staring at something, scratching your head, thinking ’something’s not quite right here’ or seeing a pattern you weren’t really expecting. This thought also comes up in passing in the lecture I’m going to offer you below.

Steven Johnson presents his exploration of the source of good ideas in two different videos, one a stage presentation for a TED lecture (first video below), the other I can best describe as a whiteboard narrative.

He is interested in the environments that promote creativity. What are the settings, the places that encourage new ideas to arise.

Listening to his lecture reminded me of things I’ve read or thought about earlier. I’ve elaborated some of these after the video, as so not to get in the way of those that want to rush in.

YouTube Preview Image

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LyX for free word-processing Grant Jacobs Sep 27


There are several free word processors available. Many are mimics of Microsoft Word to one degree or other. One alternative is LyX, a what-you-see-is-what-you-mean (not see!) document processor.

It’s free and very capable.


During my Ph.D. studies Word (version 5.1a) came with a printed manual. That’s right, a book. I read it. Cover to cover. (Crazy, but then I was a Ph.D. student.)

One of the tips for working with large documents that I took from somewhere – I think it was that manual – was to never type in blank lines as spacing: always, every last time, use the style sheets to layout the page and you’ll be better off in the end. (No backtracking later to hack fixes to individual pages when you decide to change something.)

LyX works like that. You just type text, and tell it what each block of text is: a header, the author’s name, standard body text, … You can do all of the ‘expected’ things: create tables, insert graphics, make bulleted or numbered lists, and so on.

Different document processors use different file formats for storing their output. Word has .doc files, many programs use RTF (Rich Text Format). LyX rests on TeX, a type-setting system with a long history. You don’t have to worry about that for most usage of the program. Just type away and style your document. You can export LyX documents as Word, HTML (web page), PDF, PostScript and LaTeX. (It does not export to RTF format.)

You can think of LyX as a two-level tool for document processing. Those that don’t know TeX can treat it like they would most word processors. Those that know TeX (which takes a bit to learn) can get considerably more out of the application and take their use of it to another level.

You must have TeX installed. That in itself isn’t too bad. The kicker is that a full installation of TeX is huge, a gigabyte-plus to download. (As an example, the latest version of MacTex just out is 1.6Gb.) There are much more compact versions available (e.g. ~92Mb for MacTex), which I’ve never tried. You may wish to start with them first if you want to explore.


Reference management is a job every scientist (and, hopefully, science writer) will be familiar with. Reference managers are a topic for other articles, but here I’d like to re-assure that LyX won’t leave you short on this. BibDesk, which I am currently using, and JabRef work with LyX. Mendeley may too. (BibDesk also outputs EndNote and Word format files.)

Other computer-related articles on Code for life:

Apple tip: kill Flash in Safari without quitting Safari

Consumer brain-computer interface

Web browsers (part 1)

iPads for the disabled

The iPad: a cat toy?

Local documentaries: NZ bats, Dunedin stadium and 1080 Grant Jacobs Sep 25


Tomorrow the local television channel, Channel 9, features two documentaries that might interest local readers. One covers the use of 1080 to control pests, the other the covered stadium under construction.

Let me first start with a short documentary that I encountered while researching for this post, which show great footage of New Zealand bats and discusses the impact of 1080 control on assisting conservation efforts to help them. I’ll confess it is the footage of the bats that appeals! They look great little beasts.

YouTube Preview Image

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Lazy Saturday videos Grant Jacobs Sep 25

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There are great questions asked by the public in these two videos offered by the well-named SIXTΨ SγMBΦLS.

I mean, what would happen if you stuck your hand in the beam of the Large Hadron Collider…?

And just what gets astronomers’ goat?

They’re good questions and well answered, particularly if you remember they’re speaking off-the-cuff!

YouTube Preview Image

YouTube Preview Image

If you’ve really got time to kill, I would encourage you to explore SIXTΨ SγMBΦLS’s excellent collection of physics and astronomy videos. You could lose a day in there.

(H/T: @bengoldacre and @edyong209)

Other articles on Code for life:

Varmus on writing, Autism, infographics, NCEA, cartoons and much more

Career paths, redux – the academic research career is the exception

Friday reading – Legionnaires’ Disease, human ash sculptures, and more

Book sales, frumpy readers, and mental rotation of book titles

Apple tip: kill Flash in Safari without quitting Safari Grant Jacobs Sep 24

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It’s Friday. Temporary freedom!

(Looks around furtively.)

I can post something that’s not science can’t I?

Nevermind the silly introduction. Below is a quick tip to a common problem for users of the Safari web browser.

Update: This tip applies to Safari versions 5.0 and earlier. As of Safari 5.1, Flash is a plugin.

Kill Flash in Safari without quitting Safari

Safari is Apple’s web browser. I’m probably more a fan of Opera than Safari, but Safari is the default web browser for Apple computers. Not that that means much given the ease you can install any of the alternatives but, let’s face it, we’re all lazy. One huge drawback is that Adobe’s Flash seems to induce hangs. Here’s how you can kill Flash if Safari starts to beachball:


  • Open Activity Monitor (under Utilities).
  • Show the processes by ’All Process, Hierarchically’.
  • Locate ‘launchd’ (the launch daemon).
  • Within this should be WebkitPluginAgent, within that FlashPlayer.
  • Double click on FlashPlayer, then click Quit.
  • You’ll be offered to force quit Flash. Done.

You may want to close or reload the offending browser window or tab that triggered the stall.

(Updated: somehow the first line got dropped. Don’t ask…)

Other computer-related articles on Code for life:

Consumer brain-computer interface

Web browsers (part 1)

iPads for the disabled

The iPad: a cat toy?

Varmus on writing, Autism, infographics, NCEA, cartoons and much more Grant Jacobs Sep 23


Before settling down to some more lengthy science – I know I keep promising this, but I’m having a funny old time at work – here’s a round-up of interesting reads I’ve run into over the past week or so.

Varmus on writing Harold Varmus has written in the Washington Post in particular about writing, leading with a potted (and interesting) autobiography.

Autism Readers interested in autism may wish to explore the LA Times feature Autism in LA. There’s enough to keep you going for all evening there.



Attention New Zealand university lecturers How many (New Zealand) university lecturers know if their institution is tracking changes in the science curricula and inform them of these? Alison recent wrote about science high school teachers, the change in curriculum. A question I had was how well these changes reach the lecturers, so that they might adapt their courses well in advance. If this affects you, I’d speak up!

It’s the Old Spice Guy… Only scicurious could write this. Yes, it’s the Old Spice guy… a gel advertisement like you’ve never seen before, in a blog post.

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