Archive October 2011

The coders’ quotation quandary Grant Jacobs Oct 31


Seen on twitter:

Coders are special. ’We are expected to know how to do things we’ve never done before and estimate how long they will take.’

Offered to readers with no comment.

What do scientists want from politicians? Grant Jacobs Oct 30


In New Zealand, election madness is upon us.

The various parties are pitching their promises.

What do scientists what from political parties?[1]

To get the conversation going, a few starters are listed below.

I’m not saying these are all sound or that I even endorse these. They’re offered to encourage tongues to waggle or, more accurately, fingers to type into that comment box below in the hope that more practical suggestions than my feeble efforts emerge.

Humourous contributions are welcome too! Serious policy can get too staid… Non-scientists are welcome to offer thoughts, too. Read the rest of this entry »

Wolinsky, Kendrew and others on science blogging Grant Jacobs Oct 28

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Freelance journalist Howard Wolinsky has written an examination of science blogging, More than a blog, published in EMBO Reports. It will be open access until December (2011) – get in while you can!

Wolinsky’s article presents views gleaned from leading science bloggers including Carl ZImmer, Rosie Redfield, PZ Mysers, GrrlScientist, Jerry Coyne, Sean Carroll, Bora Zivkovic and several others.

Also on science blogging is Sarah Kendrew’s article presented at the Guardian blogs, Brian Cox is wrong: blogging your research is not a recipe for disaster. Whilst relating the example of the faster-than-light neutrino work she mentions that this is still not peer-reviewed. How many readers knew that? – I didn’t. Read the rest of this entry »

Royal Society ‘aged’ back catalog free, permanently Grant Jacobs Oct 27



There’s going to be some happy science historians, including amateur ones. (And just plain ol‘ scientists, too.)

Phil_trans_indexReaders who have followed this blog for some time, might recall me writing about the Royal Society of London opening it’s full collection for a period in 2010.

The Royal Society website has now announced that the back catalog for work older than 70 yeas old is open to anyone, free of cost, permanently.

Great stuff.

The opening of this ‘aged’ portion of the archive is timed to coincide with Open Access Week, promoting promoting Open Access scholarship and research.

Read the rest of this entry »

When a City Falls – trailer for movie on Christchurch earthquakes Grant Jacobs Oct 26


Below is the trailer for a feature-length documentary on the earthquakes at my hometown, Christchurch, When a City Falls, directed by Gerard Smyth.

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Bioinformatics – QC, reproducible, statistical and sequence-oriented Grant Jacobs Oct 26


For bioinformatics geeks, or biologists interested in it: a few ruminative thoughts and one concern – should more attention be paid to different areas of (computational) biology complementing eachother?

A few weeks ago I attended the bioinformatics satellite meeting of the annual Queenstown Molecular Biology Meetings, locally known as the QMB meeting.

If there was an over-arching theme, it would have been QC (quality control) with some some aspects of reproducibility woven within it, but a discussion at toward the end left me a little concerned.

As someone who has been long being arguing for better QC it was good to see several talks on this (although the repeating of the theme gave the perhaps misleading impression of a sudden rush of enthusiasm for it).

QC in many ways is simply care and attention to detail over your data: ensuring you understand what it is able to, and not able to, convey. Formal QC helps ensure you catch any gaffes before you ship the results. Good stuff, in other words.

Reproducibility, something I’ve been a fan of since my Ph.D. student days, also featured.[1] It’s particularly important with large datasets being made accessible to later (re)analysis, including by other research groups.

So far good, but one concern emerged from listening to an open discussion in which people referred to bioinformatics work: the only examples raised were from sequence analysis, especially high-throughput analyses, and the statistics associated with that.

While it will in part be a reflection of the earlier presentations, in the way that conversations tend to follow earlier leads, I wasn’t especially happy with this as bioinformatics is more than just stats and sequences.

Read the rest of this entry »

The neutrino song Grant Jacobs Oct 23

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… in Irish folk rock. (Band Corrigan Brothers, featuring Pete Creighton.)

Who says current science never makes into song?

YouTube Preview Image

(Lazy Sunday post, this. Now I’m off outside – beautiful Spring day.)

What books do you think geeks should read? Grant Jacobs Oct 22


Wired has posted a list of nine books they think every geek should read. I’m left wondering what my readers would suggest are the books every geek should read.

Those on Wired’s list are not all ones I’d have chosen. That’s not very surprising, of course – we all have different tastes.

Godel-Escher-Bach-cover-250pxI certainly wouldn’t have included the first on my personal list of  nine to recommend – Advanced Dungeons & Dragons Dungeon Master’s Guide. Nor the comic book series Watchmen.

That’s not to say that I didn’t read comics as a kid – we used to trade them down at a corner book exchange a few blocks away from our house. I also played the text-only adventure games Zork, with their geeky puzzles.

Books I have read on their list are Gödel, Escher, Bach: An Eternal Golden Braid, The Hitchhiker’s Guide to the Galaxy, The Lord of the Rings and The Visual Display of Quantitative Information.

Their list leans more to novels than mine probably would, perhaps for wider appeal, and I guess is targeted at present-day computer geeks rather than geeks in a wider sense. Mine would likely include more of the better popular science and lean towards targeting science geeks.*

But what books would you put in a top-nine for geeks? This is your chance! Read the rest of this entry »

ScienceWriters2011 Grant Jacobs Oct 16

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Just a quick heads-up for those interested in science writing – a joint annual meeting of the National Association of Science Writers and the Council for the Advancement of Science Writing (both of the USA) is currently underway. There’s a twitter stream under the #sciwri11 hashtag (don’t forget to select ‘All’, rather than ‘Top’, so that you can see all the tweets) and a Facebook page that you might like to follow.

While the meeting is primarily for science writers in the USA many of the issues are, of course, universal. As far as I am aware there is no live-streaming video of the sessions.

Update: There are article about some of the sessions at the NASW past event coverage web page. (Look for the subject ‘ScienceWriters meeting’ just about the article titles.)

(Earlier update to add additional reading links, below, and tags.)

Other articles on Code for life:

Scientists can’t write?

When the abstract or conclusions aren’t accurate or enough

Local events: science story telling, non-academic careers, doctors and evidence

Of use of the active voice by scientists

Know the history of your field, be it science or pottery

Banished from science writing. Words, that is.

Big asteroids heading towards the earth Grant Jacobs Oct 15

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For something alternative to the rugby for the weekend here is astronomer, author and science blogger Phil Plait giving a TEDx lecture at Boulder, Colorado, on those really big asteroids that have hit the earth and what we might do about those still out there if they head our way:

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