Archive July 2010

When ideas have sex Grant Jacobs Jul 19


Zoologist-turned-science writer Matt Ridley speaking from Oxford presents ’How ideas have sex’, how they join and recombine to form new creations.

If the title isn’t enough to draw you, try this sound bite: ’Homo erectus made the same tools for 30,000 generations.’

You’ve got to think about that.

More-or-less the same design for around a million years.

(The sheer monotony of it!)

Here’s the video, enjoy it:

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Other articles at Code for life:

Temperature-induced hearing loss

Scientists can sue if not happy with funding priorities??

Scientific article download costs

Oliver Sacks on Hallucinations

What is your relationship with your research notebook?

Scientists can sue if not happy with funding priorities?? Grant Jacobs Jul 18


Last week’s edition of Nature has an editorial (open access: web pagePDF file) reporting a new twist in a law suit involving Christian groups and two scientists suing US government departments over embryonic stem cell research.

The editorial has drawn a lively discussion in the comments.

The law suit, filed August last year would look to be another attempt by the religious right in the USA to ban embryonic stem cell research to suit their beliefs. The Nature editorial does not address the larger case (and neither am I here), but is focused on what they argue is specious and dangerous reasoning to allow the scientist plaintiffs to stand.

Nature reports that the scientists who were initially dismissed as plaintiffs have appealed, justifying their interest in the case through arguing embryonic stem cell research is competing with funding in their area, adult stem cell research:

To justify their standing as plaintiffs, they argue that because federal funding is now going towards research on embryonic stem cells, there are fewer funding dollars – and therefore ’increased competition’ – for research using adult stem cells.

As the editorial goes on to say:

It is hard to say which is more disturbing – the argument made by the two scientists or the fact that it was accepted by the court. Both issues set a dangerous precedent by suggesting that researchers are legally entitled to a certain portion of the funding pie, and that changes in a federal agency’s research priorities – which often occur as scientific disciplines evolve – open the agency up to lawsuits.

Taken at face value,* and writing just a little tongue-in-cheek, this would seem to amount to allowing envy to be a valid reason to be in court. (’Aawwh, they’re getting the money I’d like to have.’)

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Walking with Rex Grant Jacobs Jul 17


(Source: RexBonics.)

(Source: RexBonics.)

In the news over the past few days from New Zealand is Rex, an exoskeletal robotic leg system for paraplegics.

It’s often said that (hard) science fiction inspires the future and RexBonics’ robotic legs are no exception, apparently inspired in part by Sigourney Weaver’s character in Alien using a robotic exoskeleton to fight off an alien.

(Listening to the interviews, it is clearly more inspired by the people who might benefit, including one of the developers.)

The name Rex comes from robotic exoskeleton and is the result of seven years development by the Auckland company backed by local investors No 8 Ventures.

As you can imagine this has sparked a lot of discussion, including criticism.

For a  very quick view (38 seconds) of Rex in action, this from Russia Today:

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A more detailed coverage with interviews is provided by the New Zealand Herald (3 min. 56 sec.):

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Other articles at Code for life:

Scientific article download costs

Temperature-induced hearing loss

Science bite: Longevity gene study has flaws?

iPads for the disabled

Minorities, disabilities and scientists

Scientific article download costs Grant Jacobs Jul 17


A brief look at the range of costs of downloading a scientific article.

I never really take that much notice of per-article fees. It’s not as if I ever pay them.

As a diversion from writing, I did a very lax survey of sorts of a small number of biological science journals. (I’m a biologist, so I’m sticking to what I know.)

What tipped me off was that while writing an earlier article I noticed that the cost to ’rent’ one of the papers was $US0.99. (This diverts to the DeepDyve website, which enables you to read the paper for up to 24 hours. One subscription option gives 25 articles for $US19.99. The first three rentals are free.)

By contrast the cost of purchasing the articles in my earlier blog article directly were:

The Carbohydrate Research article is only 3 pages long, which would work out at $US 10.5o per page.

On top of these fees would be credit card fees and current exchange costs for those outside the USA.

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Friday photo, links and video (16th July 2010) Grant Jacobs Jul 16


The end-of-the-week round-up of those open tabs…

But first the photo of the week, the rings of Saturn in the distance behind Lutetia photographed in Rosetta’s flyby of Lutetia. For more details see the Rosetta blog.

(Source: The Planetary Society blog.)

(Source: The Planetary Society blog.)

OK, now those links:

And a video, from NASA, Interstellar Clouds And Dark Nebulae (great viewing):

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Other articles in Code for life:

What famous writer do you write like?

Describe your fantasy institute

Honey’s anti-bacterial properties found?

Temperature-induced hearing loss

Boney lumps, linkage analysis and whole genome sequencing

Framing the post Grant Jacobs Jul 16

1 Comment

(Not that kind of framing.)

Late night-night thoughts on ensuring that readers come away with the message of the article.*

Jeremy Yoder writing from Denim and Tweed, following Dave Munger’s lead, frets about how

online publishing and dissemination methods can strip the nuance from scientific news

Yoder notes Munger’s point about

careful consideration of both the nut graf sent out via Twitter and RSS and the audience receiving them

He agrees (and I do too), but goes on to argue that some subjects may be less suited to blogging, writing

But the longer a post is, the more possibility there is that some fraction of the readers will quit reading before the end, and maybe even pass on links or comments based on that incomplete understanding.

Munger’s original concern (as I read it) was readers taking away over-simplistic, even mistaken, meanings from a story.

While taking Yoder’s point that short articles fit with blogging, I have to side with Munger on this issue, who points to a well-constructed dek, or sub-head, as a point that makes a difference. In particular, I see this as overcoming some of the limitations of longer articles and I can’t help think that for some (not all) types of articles the absence of a sub-head, or a poorly-written sub-head, is a key issue with longer on-line articles.

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What famous writer do you write like? Grant Jacobs Jul 15


Go to I write like, paste in a sample of your writing and let us know!

You also get a badge (icon) you can place in your blog or website if you’re into that sort of thing.

I pasted in the articles in the ‘more articles’ links at the end of this post. Here’s what writer’s works it considers them most similar to:

  1. Douglas Adams
  2. Margaret Atwood
  3. Isaac Asimov
  4. Chuck Palahniuk
  5. Stephen King
  6. Dan Brown

I’m all over the place!

Ah, well… (Maybe I could say I have a gift of writing in many styles? Nah. Somehow I don’t think anyone is going to buy that one!)

The analytical – scientist – part of me wonders if it’s affected by the subject matter to some extent. GMOs: Margaret Atwood; mental rotation: Douglas Adams; notebooks: Dan Brown…

Maybe this works better for fiction? After all I’m comparing non-fiction with fiction.

Either way, it’s fun to try.

So, what famous writer do you write like?

Bonus quiz

A similar thing is the quiz to test what kind of science writer you would be that GrrlScientist put up earlier this year.

Other articles on Code for life:

  1. Book sales, frumpy readers, and mental rotation of book titles
  2. GMOs and the plants we eat: neither are ’natural’
  3. The inheritance of face recognition (should you blame your parents if you can’t recognise faces?)
  4. Monkey business, or is my uncle also my Dad?
  5. I remember because my DNA was methylated
  6. What is your relationship with your research notebook?

Honey’s anti-bacterial properties found? Grant Jacobs Jul 14


New research suggests that (some of) the secrets to honey’s anti-bacterial properties may have been revealed.

A Dutch team of microbiologists propose that the anti-bacterial properties of the honey they tested come down to four chemicals and one general property:

Honey comb; near the top-centre bees can be seen entering the combs (Source: Wikimedia Commons.)

Honey comb; near the top-right bees can be seen entering the combs (Source: Wikimedia Commons.)

Sugars High concentrations of sugars have long been known to have anti-bacterial properties and are used in preserving food.

The best known effect is by soaking up water. Bacteria, like most living things, need water. Soak up the water and they’ll dehydrate.

Ever tried to clean up a wine spill in the carpet by dribbling some water over the stain, then sprinkling salt over the water? You’ll know how the salt sucks up the water from the carpet.

In a similar way, high concentrations of sugar outside cells, can suck water out of the cells or absorb other moisture that’s around. This works through creating an osmotic gradient, where the moveable part – water – moves to balance the low concentration of water outside the cell, dehydrating the cell.

H2O2 Hydrogen peroxide is a bleach used in making paper among other things. Household bleach kills bacteria, so does hydrogen peroxide.

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Temperature-induced hearing loss Grant Jacobs Jul 14


Two recent studies independently report mutations in the otoferlin (OTOF) gene are the cause of a rare temporary hearing loss caused by a high body temperature.


I have a hearing loss, and if I spot research on deafness when updating papers for my own research (see Footnote of previous post) I often take a peek.

Tonight I learnt that some people have deafness that is dependent on their body temperature, with a high temperature (say, a fever) inducing deafness. They recover some time after their body temperature has returned to normal.

In some ways it’s quite quirky, but knowing how molecules interact I can imagine how this might be possible.

The study I ran into was a Chinese study examining a collection of 73 Han Chinese patients with auditory neuropathy*. During this study, they uncovered a case of temperature-dependent hearing loss:

However, his hearing was affected by a slight change of body temperature. His mother found that his hearing in the morning is generally better than in the afternoon, and temperature measurements showed that his body temperature in the afternoon was generally 0.1-0.6˚ [˚C?] higher than that in the morning.

They tested his hearing loss, raising his body temperature during an extended hospital visit and found that

When his body temperature rose above 36.5°C, the boy’s hearing loss was severe (70-80dB HL) and this symptom could last for a whole day.

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The scale of cellular life and compacting chromosomes Grant Jacobs Jul 11

1 Comment

It’s hard convey the scale of very small or very large things by just quoting measurements as the measurements don’t relate well to our perception of everyday objects.

Snapshot from infographic (Source: University of Utah.)

Snapshot from infographic (Source: University of Utah.)

This interactive infographic presented by the Genetic Science Learning Centre at the University of Utah lets users zoom in from small everyday objects to the components of life. (To zoom in, drag the slider below the image.)

Below the interactive graphic are some explanations that are well worth reading.

One outlines why a sperm head is not much bigger than the (mitotic) X chromosome they show (see illustration to left):

How can an X chromosome be nearly as big as the head of the sperm cell?

No, this isn’t a mistake. First, there’s less DNA in a sperm cell than there is in a non-reproductive cell such as a skin cell. Second, the DNA in a sperm cell is super-condensed and compacted into a highly dense form. Third, the head of a sperm cell is almost all nucleus. Most of the cytoplasm has been squeezed out in order to make the sperm an efficient torpedo-like swimming machine.

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