Archive November 2010

Beauty in biology – green fluorescent protein Grant Jacobs Nov 28


Alison has challenged me to present a biology image to match her offering. For the second time I’ll concede defeat before I’ve begun…

It’s often said the beauty lies in symmetry and elegant lines. Rather like the pleasing form of an attractive body.

I’m going to offer you the symmetry and pleasing curves of this cartoon of green fluorescent protein -

(Source: Tsien Laboratory.)

(Source: Tsien Laboratory.)

Read the rest of this entry »

But what about why it’s “no”? Grant Jacobs Nov 27


From SMBC comes this cartoon of a rule for science journalism:

Don't write no articles

But, but, but … what about articles that explain why it’s ’no’?

In the background, readers hear the sound of a can of worms opening…

(Some might suggest the problem lies more with the titles than the articles, perhaps. I’m still pondering it.)

Leaving aside the science journalism question, if you like xkcd check out SMBC. Great stuff there.

Other weekend fare from Code for life:

Friday fare

Fainting kittens – feline myotonia congenita?

The best places to read

Rain, sleet, snow, music and science blogs

Find a home for your research paper, authors, related papers – ask Jane Grant Jacobs Nov 25


Jane here is not a woman’s name, but the Journal/Name Author Estimator.*

You take your abstract, plug it into a text field on the Jane web page, and press ‘Find journals’. Alternatively you can find authors or find articles.


Jane will take the words in the abstract and search a database built from Medline to locate the first 50 articles that are most similar to your abstract and from these suggest a journal, authors or related articles as a list ranked by matching scores.

As their blurb says, it as several applications:

Have you recently written a paper, but you’re not sure to which journal you should submit it? Or maybe you want to find relevant articles to cite in your paper? Or are you an editor, and do you need to find reviewers for a particular paper? Jane can help!

Read the rest of this entry »

In response to Garth George’s dig at science… Grant Jacobs Nov 21


SUNDAY RANT: A local media columnist throws a few brickbats at science. I toss a few back and give thanks for good comments.

Catching up on the New Zealand Herald website science page, which occasionally features our own work, I see that commentator Garth George recently chose to make science his rag doll for a day.

Maybe it was a slow day at the office and he simply ran out of better ideas?

Then again, looking around the ’net this doesn’t seem to be new for him. (I’m not in the habit of reading his column, so I wouldn’t know of-hand.)

But whatever.

Let’s look at what George has to say, what was said in reply, and add a few of my own thoughts.

While the title may not be his, it sweeps with a very broad brush indeed: ’Research offers little to human wisdom’ as if all research were useless.

Well done to whoever wrote the title.

Let’s consider George is only poking at human behavioural science as the first paragraph intimates.

In the opening paragraphs, I’m unsure who George is trying to slate: news editors, researchers, or both :-

Day after day in this newspaper and others we are presented with stories in which the first sentence ends with the words “a new survey shows” or “new research reveals” or “scientists have discovered”.

These items seem to have an irresistible appeal to news editors seeking urgently to fill inconvenient holes in news pages.

Few of these “research” results add anything to the sum of human knowledge for often all they do is confirm “scientifically” what we sentient humans have known either intuitively or by experience ever since we put childhood behind us.

Few would disagree with the first paragraph: tired ways of presenting science aren’t helpful. Some of the editorial choices do leave science-savvy readers wondering. The third, though, reveals a lack of understanding of why research is done.

Read the rest of this entry »

Desk Guide for Covering Science, and academic conferences Grant Jacobs Nov 21


Introducing a booklet covering science journalism and academic conferences.

This week saw the release of the New Zealand Science Media Centre’s Desk Guide for Covering Science. Journalists and those interested in science writing should get to it!

It’s small, colourful booklet packed with tips. While targeted at New Zealand journalists, the general advice will apply to all.

Like all condensed presentations there is plenty that could be expanded upon if you had space.

I thought I’d use their publication as an excuse to write a little about academic conferences for those not familiar with scientific meetings, taking my cue from the seventh of the BBC’s Pallab Ghosh’s top ten tips for reporting on science stories quoted on page 27:

7. Unpublished is okay. Research doesn’t always have to be published for you to report on it. Research presented at scientific conferences won’t have gone through the rigorous checking processes it would have if it were published in a journal.

But, because the work is being presented in a public forum by reputable scientists, science journalists do report these stories. During national emergencies, leading scientists are called upon by government to carry out research to help tackle the problem. Because of the urgency of the situation, there’s no time to put the research through the normal checking process.

But we do report this research because it has been informally assessed by leading experts.

Read the rest of this entry »

OMG* Grant Jacobs Nov 20


* Oh My Goodness.[1]

Pointers to a few of the less ordinary things I’ve seen on-line over the past day or two.

Alcoholic energy drinks, containing a mix of caffeine and alcohol, are not the way to go. There’s been a number of articles on the levels of alcohol in caffeine drinks and the effect of mix (reportedly more potent than alcohol alone). This article in the LA Times looks at why alcohol and caffeine is a deadly mix. Consider this quote:

Scientists aren’t sure exactly how the body processes the combination of caffeine and alcohol because the combination – at least in the quantity seen in these alcoholic energy drinks – is too dangerous to test on humans in scientific experiments.

Hmm? (True?)

It makes me wonder what the situation in New Zealand is with these type of drinks.

(Whilst getting this sorted, I ran into an excellent story from Deborah Blum in Slate, telling how US authorities countered bootlegging with spiking the alcohol sources.)

University rankings Egypt’s Alexandria University has shot up the international university rankings, apparently largely at the hand of a single researcher who published ’320 of his own articles in a scientific journal of which he was also the editor’. (I can’t help thinking that they ought to revise the scoring so that it weighs down rare outliers, so that the scores reflect the institution as a whole, rather than being susceptible skewing by a few individuals.)

Carnal Carnival Lead off with a title opening ’OH YES! YES!! YES!!!’ the theme this month is – well, you guessed – orgasms. Check it out. You know you want to. Of course, it also shows that scene from When Harry Met Sally.

Front line medical infections Wired has an article relating how front-line medical teams are exposed to infections from those they seek to assist.

Caveat tweetor? Twitters might take note. Apparently, China has sentenced a year of hard labour for a re-tweet. Yikes.

Dawkins reads hate mail in this fire-side setting. (YouTube video.) I get the rare crank mail, but no way near what he gets. The most recent was a comment that in it’s entirety reading ’DELETE THIS F**KIN POST’ (modified, with asterisks replacing a few letters) and some rather skewed ’science’ sent through my contact form.


[1] I know it’s usually Oh, My G-d. Seeing as the expression conveys surprise, I prefer to do that directly without evoking something I don’t believe in.

Other lighter fare on Code for life:

Friday fare

Another one bits the dust: Goodbye Walkman

Fainting kittens – feline myotonia congenita?

The best places to read

Science, bloggers, activists, and science as ’the one true global culture’?

Should media only report facts and leave interpretation to the universities? Grant Jacobs Nov 19

1 Comment


Read the rest of this entry »

Professor Richard Quinn responds to exam cheats Grant Jacobs Nov 19


I really don’t know what words to put to this. Class cheats on exam, Professor let’s them know what he thinks, and offers a deal:

YouTube Preview Image

Update: To be clear, this is from the University of Central Florida.

Other articles on Code for life:

What do you want in a Head-of-Department?

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

What aspects of biology need to be explained better?

Professors, lost souls with great oratory power?

Google’s sneak preview and encryption features Grant Jacobs Nov 18

1 Comment

While writing a new blog article, I have been using Google’s new ‘sneak preview’ feature. You might not know this exists as it’s not immediately obvious. (To my mind, anyway.) For those that aren’t familiar with it, here’s how it goes.

If you run a Google search, you’ll see a magnifying glass icon indicating which items have previews. To bring up the preview, just click any of the white space around a search result and it’ll show a snapshot of the matched page to the right with the matching text highlighted:

google sneak peek w pointer

You’ll see the magnifying glass icon embolden as you roll over space that if you click will bring up the preview. Once you’ve brought up one preview, you can hover your mouse over other search results to bring up their previews. Click again to toggle the previews off.

Read the rest of this entry »

What aspects of biology need to be explained better? Grant Jacobs Nov 15


Sean Carroll, writing at Cosmic Variance, asks:

What is the one concept in science that you really think should be explained better to a wide audience?

His being a physics-based blogs, many of the answers relate to physics.

Mine being a biology-based blog, let’s try this with a biological focus:

What is the one aspect in biology that you really think should be explained better to a wide audience?

Read the rest of this entry »

Network-wide options by YD - Freelance Wordpress Developer