3D animation for teaching ecology and evolution

July 29, 2010

The Plant Ecology and Evolution group at the University of Vigo in Spain has been making 3D animation videos about their research, which are free to download for teaching purposes.

Here’s a sample of their work, showing how lizards disperse seeds

A full list of their videos is available on their website.


Dangerous scientists?

June 28, 2010

The Guardian UK Science Blog has a interesting report on a recent European survey on public attitudes towards science. The Eurobarometer survey for the European Union found that hearteningly, 80% of Europeans are interested in science, but somewhat more worryingly, that 53% think scientists are “dangerous” .  Scientists from universities and government organisations were more likely to be regarded as qualified to explain scientific and technological developments than either scientists working in industry or newspaper journalists.  The survey also found that a majority of people think that scientists don’t put enough effort into informing the public about new developments in science.

The full article is here.

When is a gene really an allele?

May 18, 2010

The way some sections of the media use the word “gene” has become a bit of a pet peeve of mine.  Here’s an example from ScienceDaily:

Tibetans Developed Genes to Help Them Adapt to Life at High Elevations

Researchers have long wondered why the people of the Tibetan Highlands can live at elevations that cause some humans to become life-threateningly ill — and a new study answers that mystery, in part, by showing that through thousands of years of natural selection, those hardy inhabitants of south-central Asia evolved 10 unique oxygen-processing genes that help them live in higher climes.

Closer inspection of this research, which was published in Science last week, reveals that Tibetans don’t actually have 10 genes that are missing in the rest of humanity, what they have are different variants of the same genes.  These variants are called alleles, or haplotypes (there is a subtle difference between these two terms which I won’t go into here – but they both basically refer to different forms of the same gene or chromosomal region).  When geneticists refer to genetic variation in a species or population they are referring to the changes in the DNA sequence that results in multiple variant forms (alleles) of any given gene, the stuff that natural selection works on.

This study found that the Tibetan population have DNA changes in 10 genes that appear to be the result of natural selection.  Two of these genes, EGLN1 and PPARA have haplotypes that are significantly associated with the “decreased hemoglobin phenotype”, which is thought to be an adaptation to high altitude living.  These haplotypes appear to be selected for in the Tibetan population.  We all have EGLN1 and PPARA, but the Tibetan populations have unique haplotypes of these genes that help them live in higher climes.

This sort of incorrect usage of the word gene is pervasive in the popular media.  The phrase “the gene for” seems to be everywhere – the gene for breast cancer, the gene for schizophrenia, the gene for diabetes etc etc.  This gives the wrong impression of what these studies actually show, and is just plain incorrect.  What is actually being referred to in these studies is an allele or haplotype of a gene that we all have, and usually it is an allele that is correlated with a slightly higher incidence of the disease, not necessarily one that causes the disease.  Perhaps its time for for biologists to be more clear about what they mean by the word “gene”, and for journalists to incorporate the word “allele” or even just “genetic variant” into their vernacular.

If you want to read more about the Tibetans, the original paper is here, and an excellent summary of it by Razib Khan at Discover Magazine is here.

Carnival of Evolution and Research Blogging

January 26, 2010

I just discovered a blog carnival some of you might be interested in.  The Carnival of Evolution is out monthly and collects some of the most interesting posts on evolution from throughout the blogosphere.  January’s edition was hosted by Observations of a Nerd, and submissions are currently being sought for February’s edition (out on Feb 1st at Skeptic Wonder).

In other blogging news, you may have noticed that some of my posts have the Research blogging icon – the green tick – on them (and if you’re reading this on Sciblogs, many of the other bloggers use this too).  This indicates that I’m blogging about published, peer-reviewed research and the post also appears on the Researchblogging.org website.  Researchblogging.org collects posts from over 1000 different blogs so is a great place to go to read about published research that might not otherwise make its way out of the scientific literature.  

Anyway, Researchblogging.org is now giving out awards (and cash!) to celebrate the best in research blogging – there are all sorts of categories, including best biology blog, best blog post, and best research twitterer.  So head over there and nominate your favourite research blog (hint hint!).

Science podcasts

October 10, 2009

For those of you who prefer to get your science in aural form, I thought I’d share a couple of excellent sites for podcasts.  Both of these sites succeed in making science entertaining for the public, covering both breaking science stories and discussing the science of everyday phenomena. 

The Naked Scientists are a group of researchers from Cambridge University who produce a regular science show for the BBC.  Each episode is around 30 mins long and covers a handful of different science stories at a snappy pace, often with the help of an expert guest.  You can download the podcasts of their show from their website, which also has some cool articles, ideas for experiments you can do in your kitchen, and a forum where you can ask your favourite random science question.

Radiolab is a US-based science show, broadcast on public service radio stations across the US.  Each hour-long show covers a particular aspect of science and/or philosophy, and uses music, sound effects and a healthy dose of humour to get the point across.   Podcasts of the shows are available from the website.  For those of you with short attention spans, there are also short podcasts (15-20 mins long) on the website.

Warrior genes and the disease of being a scientist

September 15, 2009

The past few days, headlines like “Maori don’t have warrior gene” and “Maori warrior gene debunked” have been all over the media. This has left me with a sinking feeling in the pit of my stomach, and thinking that this sounds a lot like media hype/oversimplification of what is a very complex area of research.  To recap…

Back in 2006, Rod Lea gave a presentation at the 11th International Congress of Human Genetics showing that Maori have a higher frequency of a particular variant of the Monoamine Oxidase-A (MAO-A) gene.  In some studies, this particular variant has been linked with aggression and antisocial behaviour, and one study back in 2004 dubbed it “the warrior gene”.  The media picked this story up, and bandied around headlines like “Warrior gene blamed for Maori violence”, making statements claiming that “New Zealand Maori carry a “warriorgene which makes them more prone to violence, criminal acts and risky behaviour”.  This is not what Lea and colleagues claim in their original study at all – I’ll talk more about that below.

Anyway, now according to media reports this claim has been “debunked by science”.  When I read this my initial thought was that someone has done another study of Maori MAO-A allele frequencies, and found conflicting results.  But actually this is not the case at all.  The “scientific study” that debunks this claim is actually just a review by Maori academic Dr Gary Hook, published in Mai Review – a peer-reviewed journal of Maori and Indigenous development, but not a scientific journal.  Hook makes some good points, which I’ll talk more about in a minute, but presents no new data and much of his review of the scientific controversy has already been covered in a previous article.

Read the rest of this entry »

Conferences, and why I won’t be blogging from mine.

July 9, 2009

The North American conference season is upon us and my colleagues are leaving left right and centre for their favourite excuse for escaping the NZ winter.  My excuse this year is the Gordon Conference for Ecological and Evolutionary Genomics, a small meeting held in the woods of New Hampshire. 

There’s been a bit of talk around lately about people using blogs and twitter to report from conferences, initiated mostly a small furore surrounding Daniel MacArthur of Genetic Future blogging from the Cold Spring Harbour Biology of Genomes meeting (read his take on it here).   The issue here was that mainstream science reporters attending the meeting had to obtain permission from the speaker before writing about their work, but for scientist-bloggers like MacArthur there was no such requirement.  Nature then weighed in with an article discussing the pros and cons of allowing details of conference presentations (which often include preliminary, and almost always non peer-reviewed results) to be disseminated far and wide through the social media.   

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