Archive 2010

A holiday message to my readers Grant Jacobs Dec 24



Read the rest of this entry »

Is New Zealand’s biz/collaboration isolation reflected in airline statistics? Grant Jacobs Dec 21

1 Comment

Don’t get me wrong, I’m not knocking my own country! Far from it.

This sentence from Rod Oram’s opinion piece touting Air New Zealand’s success in recent years struck me as possibly reflecting a different pattern of business travel from New Zealand as to other nations:

Overall it [Air New Zealand] is only the 45th largest airline in the world but it ranks 11th in flights over 10 hours. Moreover, it has an unusual passenger mix: far more people travel with companions and on holiday, and fewer alone and on business compared with other long-haul airlines. [Emphasis added.]

Note that this is comparing long haul airlines, not airlines dominated by, say, short hops within Europe or the USA.

Source: xkcd

Source: xkcd

One reason I broach this seemingly unrelated subject is that science business is occasionally discussed on this forum. For academic projects* there is also the matter of face-to-face meetings with long-distance collaborators.

Read the rest of this entry »

Rate the readability of your blog Grant Jacobs Dec 20


(or anyone else’s blog or website!)

Taking my lead from Colin Schultz’s latest article who uses Google’s new readability score to rate the readability of some science blog sites and networks (but not our’s), here’s how Google ranks Code for life:


Or an averaged readability score of 1.96 (see Schultz’s article), i.e. Readability = [ (1 x Basic score) + (2 x Intermediate) + (3 x Advanced) ] / 100. (Careful readers will note the the individual percent scores are rounded, so dividing by the total of the individual percentage scores, rather than a fixed 100 might be better and leaves me with a score of 2.00.)

Google’s readability ranking rates the text in three levels: basic, intermediate and advanced. Colin’s survey shows many popular science bloggers, like me, have a majority of articles under ‘intermediate’.

To try this on your own blog (or other sites) instructions are on the Google help page. Start with an empty google search form (a brand-new search with no search terms in the URL) and put ‘site:URL’ in the Google search textbox, or search ‘site:URL’ where ‘URL’ is the site whose readability you wish to examine;* next click ‘advanced search’ (to the right of the search box); under ‘reading level’ choose ‘annotate results with reading levels’; finally press ‘advanced search’ (bottom right of page) to get the readability displayed.

Once you have set google to display the readability of the first site, it will continue to present a readability plot for each new search result until you click the blue cross below the right end of the search textbox.

You could use the year (2010) as a search term but in my limited testing it doesn’t make a lot of difference, at least not for blogs with a reasonable volume of output.

Have fun exploring the readability of your favourite blogs. As an example of what a more technical blog looks like, here’s how Mystery Rays from Outer Space fares (readability=2.89):


By contract Bioephemera leans more on the readable side (1.76):


Instead of plotting readability levels, you can limit search results to specific readability levels.

Let me add a digression. Google’s help page on this new readability option suggests ’A scientist searching for the latest findings from the experts may want to limit results to those at advanced reading levels.’ While this might help lift more formal science blog articles rise above the noise, you’d still have to eliminate crank websites. The word-based score will likely also rank crank websites as ‘advanced’ because their efforts to sound technical, and hence creditable. (Having seen silly claims for creditability from some people that follow crank websites, I wouldn’t be entirely surprised if some of these people claim ‘advanced’ readability scores indicate creditability, silly as the idea is.) Here, for example, is what we get for the articles at–as Orac might describe it–’that warehouse of woo’, (score=2.44):


I say ‘blog articles’ in the previous paragraph because to locate articles in the peer-reviewed literature, you’d expect you’d be better off with the more established means of searching the literature such as PubMed, Google Scholar or the like. As for science popularisation sites, we’ve already seen that many rate ‘intermediate’. This doesn’t mean that they are less creditable, but that they are targeted at a wider audience.


If you use Mac OS X, you may find it useful to use shortcuts to copy URLs. To copy the URL of a link control-click on the link: a pop-up menu will appear – choose ‘Copy link’.

* A quirk (read: bug) means that when you move to the advanced search from the basic search page, it’ll take the search terms in the web browser’s URL (location field)–not the textbox–into the advanced search. As a result you will want to either start with an empty search page with no search terms in the URL, or start by first searching the URL you want to test (thus moving your search terms into the browser’s location field). In my opinion Google’s form-processing software should be checking if the search testbox is not empty and if so, using these contents. Either way, you’ll have to work around this.

Older articles on Code for life (these from my first month of  blogging):

Scientists can’t write?

Book excerpt – Losing the faces of your wife and children

Autistic children and blood mercury levels

Three kinds of knowledge about science and journalism

Forgetting older science

Monkey business, or is my uncle also my Dad?

Fun with ngrams Grant Jacobs Dec 19


As everyone will know by now, GoogleLabs has created a database of words from Google Books and presented an on-line tool allowing users to create plots of ngrams.


Details of how all this works are briefly outlined in a help page and a research paper in Science.

I have to admit I think it’s pity that Google–wealthy business that it is–didn’t pay to have the article presented as open-access. (Perhaps in another journal.) Surely it’d better promote their tool if they did?

In any event, Ed Yong has this covered on his blog. Rather than review the work, I’m offering this as an invitation to amuse yourself (i.e. holiday entertainment) in a less rigorous manner as suits the season…!

Below I’ve included a small number that I have generated with a little experimenting to encourage readers to play.

Share your favourites in the comments.

Read the rest of this entry »

Christmas tree Grant Jacobs Dec 18


This one bioinformaticians (or computational biologists or computer scientists) should ’get’ immediately:

(If any non-computer science readers don’t get it, you’re welcome to ask in the comments. I personally would have drawn it with the presents on the leaves, but that’s me.)

Other lighter fare on Code for life:

Mid-week entertainment – links and news

Fainting kittens – feline myotonia congenita?

Lazy Saturday videos

Science-y reading and open book thread

Describe your fantasy institute

Too much attentiveness leads to inattentiveness

Book review – The Poisoner’s Handbook Grant Jacobs Dec 17


If you’re after a last-minute present for a fan of crime writing or popular science, preferably with a morbid bent, Deborah Blum’s The Poisoner’s Handbook* might be the ticket.

Crime fiction–that I read, anyway–usually has a forensic scientist hero struggling to solve a case, battling with local politics, bureaucracy, science and changing criminal landscapes. (And occasionally dodging bullets or other fictional threats.)


But what of the struggle to create the forensic science industry? It, too, battled with local politics, bureaucracy, science and changing criminal landscapes.

Subtitled Murder and the Birth of Forensic Medicine in Jazz Age New York, the lead characters of this work is the Chief Medical Examiner of New York City, Dr. Charles Norris, and toxicologist Alexander Gettler. Norris is appointed under strained political circumstances. His office’s story is told as more than a straight history, with each chapter titled for one poison and cases related to that poison, as well as the years covered.

In this way the book mixes intriguing case stories with the on-going political and scientific struggles.

Overall the book covers 1915 through to 1936, eleven poisons, and contains a bibliography, notes and index to satisfy those seeking further reading.

It’s often said that fact is better than fiction. One of my few gripes is that the condensed case stories leave me wanting more. That hardly counts against the book–it simply means the cases are well-written and the writer achieves her aim of sparking interest. Some things people have tried really are pretty amazing…

Read the rest of this entry »

Mid-week entertainment – links and news Grant Jacobs Dec 16

No Comments

Firstly, I’d like to apologise to my regular readers for the sheer lack of articles recently. You won’t want to know the many reasons behind it!*

I’m likely to be limited to irregular efforts until after the Xmas break; articles will happen, just not my preferred daily (or so) writing.

I’m offering this short collection of news and links to let my regular readers know I’m still around…just floundering around in a sea of chores.

You know where from (xkcd)

Source: you know where from (xkcd)

Fox News managing editor, Bill Sammon, asks (demands?) that journalists should on ’showing the controversy’:

…we should refrain from asserting that the planet has warmed (or cooled) in any given period without IMMEDIATELY pointing out that such theories are based upon data that critics have called into question. It is not our place as journalists to assert such notions as facts, especially as this debate intensifies.

Am I reading this right? An editor is telling journalists to frame what they present? Never mind that this confuses political, social and scientific controversies.

Read the rest of this entry »

Occam’s Typewriter – a new science blogging network Grant Jacobs Dec 10


A quick head’s up for those who, like me, try keep tabs on where all these science bloggers are,* there’s new science blogging network: Occam’s Typewriter.

Most of the starting line-up look to be bloggers from Nature Network, including stalwarts of that place Jennifer Rohn, Stephen Curry, Richard Grant, Austin Elliott, Erika Cule, Cath Ennis among others.**

Current posts include:

Stephen Curry: Time travel

Jennifer Rohn: In which I question my own sell-by date

Cath Ennis: Not your average cell signalling talk

Cromercrox: All you bouy are belong to us

Good luck with the new digs!

(Although I do wonder about that motto. Just what do you mean by it? I’m kidding, I’m kidding. Oh, also: in case you think you are launching a day early, it is Friday the 10th here in New Zealand…)


I’ll update my ‘Other science blogs’ page soonish (read: sometime…)

* They seem to move about so much – is restlessness a feature of scientists?

** I confess this weasel wording is ploy to avoid offending anyone I might have missed out. Feel free to add to the list in the comments.


(An update already?)

You can follow them on twitter @OccamT

Other articles on Code for life:

NASA: science shouldn’t be debated in media and blogs?!

Lecturers sitting in on colleague’s lectures, and laptops

How long does it take you to write a science blog post?

Coiling bacterial DNA

Fainting kittens – feline myotonia congenita?

NASA: science shouldn’t be debated in media and blogs?! Grant Jacobs Dec 07


A few minutes ago Ed Yong tweeted:

NASA deems it inappropriate “to debate the science using the media and bloggers” But runaway hype okay? HT @david_dobbs

GFAJ-1 grown in ‘arsenic media’ (Source: Wikimedia Commons.)

GFAJ-1 grown in ‘arsenic media’ (Source: Wikimedia Commons.)

The link points to an article on the Canadian Broadcasting Centre* website, discussing Prof. Rosie Redfield’s criticism of the research paper describing arsenic tolerant bacteria on her blog.

Some way into the CBC article, it presents this response from NASA spokesperson, Dwayne Brown:

When NASA spokesman Dwayne Brown was asked about public criticisms of the paper in the blogosphere, he noted that the article was peer-reviewed and published in one of the most prestigious scientific journals. He added that Wolfe-Simon will not be responding to individual criticisms, as the agency doesn’t feel it is appropriate to debate the science using the media and bloggers. Instead, it believes that should be done in scientific publications.

This the work NASA announced as:

Dec. 2, 2010:  NASA-supported researchers have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism, which lives in California’s Mono Lake, substitutes arsenic for phosphorus in the backbone of its DNA and other cellular components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate at the agency’s Headquarters in Washington. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.”

Since then there has been considerable media coverage, along with some scientific criticism, including of the press release and pre-release promotion, the subsequent media coverage and the research itself. In all, something of a small storm.

Read the rest of this entry »

Saturday snippets Grant Jacobs Dec 04


You won’t have missed the fuss over NASA’s their non-extra-terrestrial life, where evidence suggests that a bacteria may show signs of tolerance to arsenic received wide coverage in the media. xkcd, of on-line cartoon fame, offers this

There’s a great collection of commentary to Richard Thaler’s call for informed examples of ’things we [science] once thought were true and took forever to unlearn’, starting with this question:

The flat earth and geocentric world are examples of wrong scientific beliefs that were held for long periods. Can you name your favorite example and for extra credit why it was believed to be true?

Read the rest of this entry »

Network-wide options by YD - Freelance Wordpress Developer