Archive March 2012

Bioinformatics is a sub-discipline of molecular biology Grant Jacobs Mar 30

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Via twitter I’ve been seeing this phrase emerge from Eagle Genomics annual conference.

This shot from a presentation showing a slide titled Bottom-up bioinformatics helps clear the air a little*:


There‘s a picture of some Lego figures. No sure what going on there.

But I hope you can read the writing below the title – ’Bioinformatics is a sub-discipline of molecular biology’.

Ah, an old hobby horse – although I usually approach this by replacing ‘bioinformatics’ with ‘computational biology’. Not that there is a hard-and-fast line between the two despite previous attempts of mine to distinguish them.

A reason I prefer to put myself under the title computational biologist is to remind people that it’s biology I’m doing, not IT per se.

It’s also because there is a research as well as service, something I worry some don‘t fully appreciate. I like the notion that computational biology is just the theoretical biology on which a fair chunk of molecular biology rests.

I’d love to learn the full context of this slide.**

And what was with the Lego pieces. I mean one has a pick-axe stabbed through him. What‘s with that?

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Blogimmuniqué: 29-March-2012 Grant Jacobs Mar 30

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A blog communique – brief notes to my readers!

First up: my apologies for the temporary hiatus over the last few days. My time is being split into far too many directions… While I’m getting back on track again, I thought it’d be a good opportunity to updating people on what I’m doing, or introduce newer readers to some of what I hope to happen here.

New topics/series

First I’d like to briefly introduce a couple of several topics I hope to run in irregular fashion. These are unlikely to be a series in the more formal way, more as a thread of articles sharing a theme, perhaps under a running title. (I’m likely to run the series titles as sub-titles so that they don’t mess up the main title or make it longer than it needs to be.[1])

The first topic ‘series’ is Structures in our genomes, which follows one of my key research interests. I’d like to wind my way past different structures that are part of our genomes as one way of introducing non-scientist readers to their genomes. Genomes are often talked about as DNA sequences – I’d like to look at them as structures, which in many ways is what they really are. A proper introduction to this is in draft form at the moment.

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Seduced by logic Grant Jacobs Mar 23


My previous cat traded in a habit or two every six months or so for new ones. I sometimes think my reading does something similar.

For a last while I’d fallen into reading several books concurrently, something I generally don’t do. I’m usually a one-book-at-a-time guy. Nevertheless, while starting on the Robyn Arianrbod’s book on the history of two women mathematicians in late 19th century Britain, I was also simultaneously attempting to an eclectic mix of novels (one crime, one sci-fi) and a stack of travel guides, along with my usual scientific reading.*


Seduced by logic is Robyn Arianrbod’s biography of the work of two woman popularisers of science, Êmile du Châtelet and Mary Somerville.

Their common thread is their relationship with the ‘Newtonian revolution’. We see through the biography work that brought Newton’s science to wider acceptance.

Her descriptions of the importance of Newton’s work are, to my mind, excellent. It’s not easy to explain the conceptual basis of mathematical work using only words this clearly. Other mathematicians’, physicists’ and astronomers’ work are brought in to form the wider picture.

The historical and social contexts set the scene, with the growing intellectual (and political) freedoms from the state (or religion) presented through progress and disruptions of the players of the times. This includes the role of women, their opportunities to learn things academic and participate in academic life. There are also brief asides into issues familiar to those writing about science, as well as some interesting historical tidbits.

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The world in DNA sequencers Grant Jacobs Mar 22


Powerful DNA sequencing technology gets a lot of attention and the amount of DNA sequence data pouring out these days is impressive (and is set to rise further).

So where are these devices? There’s an interactive map of where they all are on


Click on each blue location marker for details about the centre. Clicking on circles will produce an enlarged map of that region. Along the top you can limit those shown to particular types of sequencers (not shown in the image above). Read the rest of this entry »

Teaching students to write scientific papers Grant Jacobs Mar 21


(Mid-week ramble!)

How did you learn to write a scientific paper? (Also: how did your first paper go?)

This brief thought is inspired by a discussion over at Occam’s Typewriter, at Cath Ennis’ place (aka ). There she was pointing (grumping?) at some long-winded phrases in papers she was helping others with.

Somewhere in the discussion there’s this exchange between us (links and emphases as in original):

? says:
It boggles the mind how few people seem to have read any scientific papers before attempting to write their own!

(I’m not referring to this specific manuscript, but rather to a general pattern of people just not seeming to understand the conventions of the format)

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Science blogging in the New Zealand media Grant Jacobs Mar 20


My article for today is over at Nature’s Soapbox Science.

During a recent Royal Institution discussion that I was following on-line via twitter Fiona Fox, head of the UK Science Media Centre (SMC), was reported as saying that ’blogs are fantastic but no journalists goes to them to look for full stories — must be realistic’. I thought that this wasn’t the experience of those writing here at the Sciblogs and suggested as much in reply.

Lou Woodley, on-line editor for Nature’s community forum and blogs and who was part of our on-line conversation, invited me to write a guest blog expanding on this. With the help of others writing here (huge thanks!), I have outlined some of the interactions with the New Zealand media we have experienced and offered a few thoughts as to why we experience this interaction.

A selection of articles on science communication at Code for life:

Communicating complex and post-normal science to the policy maker and the public — lessons from New Zealand

What should be taught in science communication courses?

When the abstract or conclusions aren’t accurate or enough

Of use of the active voice by scientists

Media thought: Ask what is known, not the expert’s opinion

To St Patrick’s day and alcohol Grant Jacobs Mar 18

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Yesterday was St. Patrick’s Day. As I sat reading a book in wonderful sunshine in the nearby botanical gardens accompanied by a beer (of course!) students were suspiciously wearing green. Dunedin is a university town, with all that goes with that. Every event that can be celebrated is.

Here’s a science student’s folk ode to St Patrick’s Day and Saccharomyces cerevisiae (brewer’s yeast), fermentation and all that. It’s even educational!

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A blue family Grant Jacobs Mar 17

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It‘s too late tonight to work on an article for this blog.*

In place of an article of my own, I would encourage readers to try this excellent long-form article about a Kentucky family that was blue.

Not sad, nor another case of overdoing the colloidal silver,** but a family with a genetic disorder, methemoglobinemia. It’s well worth reading. (You’ll need to skip one of those annoying adverts; just click it away.)


* I’ve been working on a piece for the Nature Soapbox Science blog; more on that when it appears.

** An alternative ‘remedy’ aimed at preventing illness on the basis that silver has anti-bacterial properties. Those who persist with this remedy develop argyria – as the silver accumulates in the body skin exposed to the sun turns grey-blue.

Other (older) articles on Code for life:

Monkey business, or is my uncle also my Dad? For male pygmy marmosets, their genetic father could be their uncle. Confused? Check it out.

Deleting a gene can turn an ovary into a testis in adult mammals I was startled to learn that ovaries may not be permanently defined to be ovaries in some adult mammals.

Aww, crap. Some pitcher plants have adapted to be tree-shrew toilets…

Finding platypus venom Researchers cleverly did not extract the venom, but created the venoms by comparing the platypus genome with known venomous proteins and expressing the genes that matched. (One of my favourites articles.)

Minorities, disabilities and scientists The silly pictures were fun. Hearing aids like you’ve never seen…

Temperature-induced hearing loss A few rare individuals have temperature-sensitive hearing, losing it when they have a high body temperature.

From dying stars to dust clouds to us – star stuff, all Grant Jacobs Mar 14


All the stuff that make up us came from stars. (Some time, ages ago.)

This meme isn’t new, Carl Sagan played it too. This is a lazy mid-week post as I’m starting to nod off toward sleep, but it’s still great to listen well-known American science communicator Neil Tyson’s excellent take on it.

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(I wasn’t quite so keen on the trailing musical portion myself, but what gives?)

Dunedin event: “Global Climate Change Treaty – Can Humanity Deliver?” Grant Jacobs Mar 14

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On behalf of the University of Otago Centre for Science Communication I would like to alert local readers to an open lecture and panel discussion on climate change policy to be held at the St. David Lecture this afternoon (Wednesday March 14th) from 5:10pm until 6:30pm.

The speaker is Professor Jonathan Boston, Professor of Public Policy at Victoria University in Wellington, presenting - ’A New Global Climate Change Treaty–Can Humanity Deliver? Our Challenge After Durban for 2015’.

There are no bookings – get to the lecture theatre early if you want to ensure a good seat.

In the second half of this event, equal time will be dedicated to open floor discussion, with a diverse panel joining Prof Boston, including:

  • Kireua Bureimoa (Physics postgrad from island nation of Kiribati)
  • Laura Black (Chief Executive, The Methodist Mission)
  • Cr Jinty MacTavish (Dunedin City Council)

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