Thursday, February 24, 2011

Images of Science

The 11th Wellcome Image Awards were announced on 23 February 2011, recognising the creators of the most informative, striking and technically excellent images among recent acquisitions to Wellcome Images, as chosen by a panel of judges.
All of the winners can be seen on the awards website. A few of my favourites are presented below.

Cavefish Embryo
Confocal micrograph of a cavefish embryo at around five-days-post-fertilization, viewed from the side (lateral view). The embryo has been stained with an antibody that targets a calcium binding protein (calretinin) shown in green, which highlights different neuronal types and their processes in the nervous system. This staining also reveals taste buds, that in the cavefish are located around the mouth and extend along the body.

The eyes are still present at this stage of development but they will degenerate naturally during the lifetime of the fish as they live in a dark environment where eyes are redundant. Thus, adult cavefish are blind.

Ruby tailed wasp
Photomicrograph of the ruby-tailed wasp. Chrysis ignita is the most commonly observed (of several) species of the ruby-tailed wasp. It is easily recognised by the vibrant iridescent colours on its body. The head and thorax is a metallic green / blue, while the abdomen is a ruby red / bronze colour, which gives it its name. The underside of the abdomen is also concave, which allows the wasp to roll itself into a protective ball if threatened.

Ruby tailed wasps are 'parasitoids' meaning that they eventually kill their hosts. Chrysis ignita parasitizes Mason Bees - the females lay their eggs in the same nest as mason bees, so, when the ruby-tailed wasp larvae hatch, they feed on the mason bee larvae. Ruby tailed wasps do have a sting but it is not functional and most species have no venom.

Cell division and gene expression in plant cells
Fluorescent micrograph showing cell division in an Arabidopsis seedling used to study in vivo gene expression and cell growth analysis, cell by cell from living tissue

Using this technique fluorescent proteins are targeted to the nucleus, so plants can be imaged as they grow, this also allows for simultaneous and automated quantification of gene activity and cell growth in a cell-by-cell basis. As the plant is alive different time points can be captured to track changes in cell size and gene activity in each cell. Information regarding cell growth and gene activity can be extracted from living tissue at different stages.

The red fluorescence is always expressed (acts as a reference), other promoters of interest are fused to different fluorescent proteins and co localized to the nucleus. In this case the green fluorescent protein (GFP) is regulated by a gene of interest (and is therefore only expressed when that gene is active and is therefore variable among cells). A third fluorescent protein is attached to plasma membrane to visualise the segmentation of cells as they grow.

Small red cells that don't have the gene active and do not express GFP are precursors of stomata. Cells that are yellow have both the red and green expressed.

Ergot fungus infection in wheat
Fluorescent micrograph showing wheat stigmas infected with the ergot fugus (Claviceps), which causes ergotism in humans.

Wednesday, February 23, 2011

Science and GM in Election 2011

The presence of the Labour Spokesperson on Science, Ruairi Quinn at an anti-GM press conference raises questions about the party's credibility on the GM issue.

At a recent talk I presented on the GM crops issue and in a recent article here and for the Guardian science blog, I suggested that the GM issue had now become an election issue.

On Monday, celebrity chef Clodagh McKenna along with people from "food, farming, conservation and human rights sectors" gathered in Dublin to speak about what their press release called the "inherent dangers of new moves to allow a relaxing of laws in relation to genetically modified food and feed". See the bottom of this post for a video from Monday's press conference.

Calling the GM "lobby" the "Anglo-Irish Bank" of the food sector, the grouping called for (amongst other things) another moratorium on GMO.

Representatives from the Irish Organic Farmers and Growers Association (IOFGA), Western Organic Network, Irish Seed Savers, and Afri amongst others met to denounce what they called a "dubious scientific review" of the GM issue.

All very predictable. It is to the direct economic benefit of the organic sector to ensure that GM does not get a fair hearing. It is to the direct economic benefit of the organic sector to scare consumers into rejecting GM food products.

It is analogous to the guy who produces white bread telling consumers that brown bread will give them leprosy - it has absolutely no scientific basis, but as a marketing ploy, it does wonders for white bread sales!
What was most surprising about the press conference was the very visible presence of Labour spokesperson on Education and Science Ruairi Quinn TD.

Labour are against the cultivation of GM crops on the island of IrelandIt is surprising given the stated position of the Labour Party on the issue.  Although Labour are against the cultivation of GM crops on the island of Ireland, they are in favour of the importation of animal feed potentially containing trace amounts of GM material.

The party's 2006 21-part plan for "A Quality Future for Rural Ireland" commits the party to "work towards the aspiration of a GMO production free island of Ireland within the context of the relevant EU and UK legislation and in the relevant national and international fora.

"Until that aim is achieved", the policy document continues, "the Labour Party will push for the strongest possible evidence-based rules governing the release of GMOs into the environment".

Two things strike me as interesting about this statement. First is the careful wording of the the first paragraph and the aspiration of a "GMO production free island", clearly not ruling out the importation of GM animal feed - as is the party's stated policy.

Secondly, the plan calls for "evidence-based rules" governing the release of GMOs. These evidence-based rules do not seem to be important when deciding the core position- that of being for or against GM crops.

While the Labour Party are to be commended on clearly spelling out their position on GM (the party line of anti-GM cultivation but pro GM  importation seems quite straightforward), the presence of the party's science spokesperson at Monday's launch suggests a different viewpoint.

Speaking at a meeting of the Oireachtas Joint Committee on Agriculture, Fisheries and Food Debate in 2008, Sean Sherlock, Labour Spokesperson on Agriculture and Food pointed out: "The EU scientific committee has applied a certain rationale which is based on common sense and practical solutions. If it is advocating a certain position [on the GM feed issue], I do not understand why the Government is not adhering to that advice or why it would abstain on votes when the time comes".

"if the EU scientific committee advises and recommends that we import certain feedstuffs, I do not see why the Government cannot approve it" - Sean SherlockThere is no dichotomy or contradiction between maintaining the biodiversity of this island and the importation of EU-approved feedstuffs. The two are not mutually exclusive. It is reasonable to express reservations about scientific trials on the growth of GM feedstuffs pending further debate and dialogue. However, if the EU scientific committee advises and recommends that we import certain feedstuffs, I do not see why the Government cannot approve it. We have all bought into that process by virtue of our membership of the EU", said Sherlock.

The labour spokesperson continued: "The precautionary principle is rolled out when it is politically expedient to do so. The Green wedge or wing of the Government has a politically philosophical position on these issues and there is a certain constituency to which it must play. This is to the detriment of Irish agriculture and ultimately the Irish consumer who will end up, if we continue on this route, paying less but without a guarantee that imported livestock or meat products from third countries are GM-free."

In a brief statement on twitter, a Labour Party spokesperson confirmed to Communicate Science that Quinn was representing the party at Monday's event and said that the party "are against growing GM crops here, but are not opposed to importing GM feed". This seems directly at odds with Ruairi Quinn's

very visible endorsement of a GM-free Ireland concept which specifically, according to the groups own press release, is also strongly opposed to the importation of animal feed potentially containing trace amounts of GM material.

it is sending senior figures to campaign for a GM free IrelandThat the Labour Party is against the cultivation of GM crops in Ireland is clearly laid out in their 2006 policy document. I would argue that there is no scientific basis for this position, but that is beside the point. What is problematic for the party is that on the one hand it is sending senior figures to campaign for a GM free Ireland - and against imported animal feed potentially containing trace amounts of GM material; while on the other hand saying that it is not opposed to the importation of such feed. 

As I've said, the Labour Party have a clear policy on this issue and while I disagree with it, they are to be commended for outlining that position, unlike a number of other parties. However, the voting public deserve to know whether or not a potential Minister for Science in the next government has rejected the overwhelming volume of scientific advice on this matter and has arguably been used as part of a marketing strategy for the anti-GM lobby.

The following video is from Monday's press conference. Ruairi Quinn sets out Labour party policy from 2:30 min onwards.

Sunday, February 20, 2011

Communicating Science: GM Crops

Well done and thank you to Cork Skeptics who organise the monthly 'Skeptics in the Castle' event at Blackrock Castle Observatory in Cork.

I was delighted to be invited to speak to the meeting on the issue of GM crops and the public perception of science and really enjoyed preparing the talk, which of neccesity was quiet different from a talk I would be used to preparing for students.

From my point of view at least, the talk went well and generated some amount of lively discussion afterwards. Hopefully I got across some of the science behind the issue and provided some food for thought.

See a write up on the talk here.

Monday, February 14, 2011

I'm a scientist... no, really!

Some great news this morning - I've been asked to take part in the I'm a Scientist, get me out of here! event in March.

According to the organisers, I'm a Scientist is "an award-winning science enrichment and engagement activity, funded by the Wellcome  Trust. It takes place online over a two  week period. It’s an X Factor-style competition for scientists, where students are the judges. Scientists and students talk online on the website. They both break down barriers, have fun and learn. But only the students get to vote".

I think this is a really great idea and I'm really looking forward to taking part. I'll keep you posted on how things go right here. The event runs from March 14th - 25th. The video below gives a flavour of what's involved.

Sunday, February 13, 2011

So, what rhymes with science?

To celebrate World Book Night, which this year takes place on Saturday 5th March, I've got three copies of Seamus Heaney's New Selected Poems to give away. I'll be giving away another 45 copies to schools and individuals in Cork courtesy of World Book Night.

To be in with a chance to win a copy of the book, and in keeping with the poetry theme, just compose a science-themed poem and submit it by email here.

It can be as long or short as you like, and any style you want, as long as it has something to do with science!

  • The poem must be entirely your own work.
  • Closing date for entry is Thursday 3rd March.
  • Judges decision is final.
  • Submit your poems here along with your name and a general location.

Saturday, February 12, 2011

Inside the Dead Zoo

To celebrate Darwin Day; a two-part documentary (via youtube) on Ireland's Natural History Museum, also known as The Dead Zoo.


Part 2

Friday, February 11, 2011

Happy Darwin Day

This coming Saturday (Feb 12th) is Darwin Day - a global celebration of science and reason held to coincide with the birthday anniversary of evolutionary biologist Charles Darwin.

You can find more information on Darwin Day here.

The following is an award winning film clip by the Wellcome Trust and presented by David Attenborough which summarises evolution in spectacular fashion. Enjoy.

Wednesday, February 9, 2011

Is GM now an election issue in Ireland?

Amidst the background of one of the most divisive and stormy parliamentary elections in Ireland's history, the outgoing government has made a significant move on GM crops.

Outgoing Minister for Agriculture, Brendan Smith, from the ruling Fianna Fáil party, confirmed in a statement this week (Tuesday, Feb 8th) that Ireland has changed its voting position and will now support a number of EU Commission proposals designed to allow for the marketing of GM food, feed and food ingredients.

The move, although welcomed in many quarters will no doubt cause controversy, not least from the ruling party's former coalition allies the Green Party, whose departure from government triggered a general election to be held on February 25th next.

Up till now, the GM issue has been absent from the debate over who should form the next government. Understandably, voters have been more worried about their jobs and the future of Ireland's economy than to be interested in the details of EU policy and rhetoric from pro- and anti-GM sides.

It's not the first time that the GM issue has impacted on this coalition government. Back in 2009, the Green Party - Fianna Fáil government had to renegotiate their terms of agreement and their programme for government (pdf). This led to a major concession to the Greens - the promise of making Ireland a 'GM-Free Zone'.

Although much trumpeted by the Greens then, it has never become a reality. Neither has the promise to introduce a GM-Free logo modelled on the German "Ohne Gentechnik" logo.

In a short response on twitter, Green Party Chairman and Senator Dan Boyle replied that the u-turn had shown “what Fianna Fáil really thinks of consumer fears” and that, in government, the Green party “had stopped this”.

Meanwhile, the Green Party’s Agriculture spokesperson Trevor Sargent said the party was “alarmed” by the move and that “in government, the Green Party ensured that Ireland abstained on this vote”.

Calling the move a backward step, Sargent said that the issue was about “consumer choice” and that the decision “damages the quality image of Irish food produce”.

Brendan Smith explained this week that "it has been a matter of great concern to Ireland, in recent years, that there has been a severe disruption to trade of animal feed, caused by the delays in the authorisation, by the EU, of GM varieties which have already been approved in the exporting countries."

According to Smith, the difficulty of importing certified GM-free animal feed  (90% of which comes from North and South America) has led to the shortfall having been made up by more expensive feed which puts Irish meat producers at a serious disadvantage. The Irish Farmers Association say this disadvantage can be as much as €15 on every pig produced.

The greens however dispute this argument asserting that “as cattle eat grass most of the year, this small premium would represent a tiny price differential for the customer (e.g. 2c on a Sunday roast)”. That’s fine, I guess if you’re eating beef and not pork on a Sunday.

Ireland's support for the EU Commission proposals was confirmed at a meeting of the EU Standing Committee on the Food Chain and Animal Health in Brussels on Tuesday.

GM-Free Ireland, had called (pdf) for Smith to vote against the proposals saying they would "undermine our Government's agreed GM-Free policy". The Irish Organic Farmers and Growers Association called the move “short-sighted” and argued that the decision did not reflect the wishes of the people.  Clearly though, with the Greens now out of government, the remaining Fianna Fáil ministers were free to make decisions without the input of their former partners.

The EU proposal seeks to remove the "zero tolerance" policy towards GM components of animal feed and allow trace amounts, up to 0.1% to be imported.

It will be interesting to see whether one of the final decisions of the outgoing administration will lead to GM becoming an issue in this election. One suspects not, but it may at least allow the public to hear from each political party where they stand on the GM issue.

The author will be presenting a talk entitled Trust Me, I'm A Scientist: Genetically Modified Crops and the Public Perception of Science to a meeting of Cork Skeptics in Blackrock Castle Observatory, Cork on Friday February 18th, 2011 at 8pm. All Welcome.

This article also appears, in an edited form on The Guardian science blog: Notes and Theories.

GM Crops & The Public Perception of Science

$1 million challenge for homeopathy

American magician and sceptic James Randi has challenged homeopathic practitioners to prove, under controlled, scientific conditions that homeopathy works. If they do, he'll give them $1 million.

See his video statement here:

Tuesday, February 8, 2011

Growing Google

A fun video on how the Google logo can be created in the microbiology lab.

My Secret Life - Friendly Numbers

My latest guest post for PBS NOVA's Secret Life of Scientists blog is now online. This week's episode features Synesthesia Researcher Steffie Tomson talking about her research and and her own experience of the condition.

You can read the post and watch the episode here.

In this month's post, I ponder the friendliness of numbers!

Friday, February 4, 2011

Little water flea has big genome

Credit: Paul Hebert, University of Guelph
The little water flea used to have pride of place on the front cover of the Leaving Certificate Biology textbook when I was going to school. Little did we realise then that Daphnia would turn out to be so impressive!

Research just published in Science shows that the near-microscopic freshwater crustacean Daphnia pulex (the water flea) is the animal with most genes (about 31,000 in total).

"Daphnia's high gene number is largely because its genes are multiplying, creating copies at a higher rate than other species," said project leader and CGB (Centre for Genomics and Bioinformatics, Indiana University) genomics director John Colbourne.

"We estimate a rate that is three times greater than those of other invertebrates and 30 percent greater than that of humans."

Colbourne postulates that "since the majority of duplicated and unknown genes are sensitive to environmental conditions, their accumulation in the genome could account for Daphnia's flexible responses to environmental change."

Much of the media coverage has centred around the fact that the water flea outstrips humans in terms of gene number (humans have around 23,000 genes). This "paradox" known as the C-value enigma or C-value paradox is based on the fact that the genome size of an organism does not correlate with the complexity of the organism.

'Daphnia is an exquisite aquatic sensor, a modern version of the mineshaft canary' - James KlaunigIt's not a new idea - the term was first used in 1971 and the solution lies in the fact that lots of DNA in eukaryotes (i.e. non-bacteria) does not code for genes. For example, only about 1.5% of the human genome codes for genes. The wheat genome, for example, is five times larger than the human genome.

Daphnia have long been studied because they can be an indicator of environmental health in freshwater bodies. "Daphnia is an exquisite aquatic sensor, a potential high-tech and modern version of the mineshaft canary", says James Klaunig of Indiana University.

"With knowledge of its genome, and using both field sampling and laboratory studies, the possible effects of environmental agents on cellular and molecular processes can be resolved and linked to similar processes in humans."

[For our Irish Readers: Does anyone have an image of the front cover of the Leaving Certificate Biology Textbook with Daphnia ? If so, let me know and I'll add it to the post]

Colbourne, J., Pfrender, M., Gilbert, D., Thomas, W., Tucker, A., Oakley, T., Tokishita, S., Aerts, A., Arnold, G., Basu, M., Bauer, D., Caceres, C., Carmel, L., Casola, C., Choi, J., Detter, J., Dong, Q., Dusheyko, S., Eads, B., Frohlich, T., Geiler-Samerotte, K., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J., Muller, J., Pangilinan, J., Patwardhan, R., Pitluck, S., Pritham, E., Rechtsteiner, A., Rho, M., Rogozin, I., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y., Yamagata, H., Yamada, T., Ye, Y., Shaw, J., Andrews, J., Crease, T., Tang, H., Lucas, S., Robertson, H., Bork, P., Koonin, E., Zdobnov, E., Grigoriev, I., Lynch, M., & Boore, J. (2011). The Ecoresponsive Genome of Daphnia pulex Science, 331 (6017), 555-561 DOI: 10.1126/science.1197761

Thursday, February 3, 2011

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Tuesday, February 1, 2011

Don't trust this blog

This blog, I think, is well written and edited. I think that each post I produce is based on solid evidence and often, it is based on one or more peer-reviewed papers which are particularly newsworthy. Nevertheless, you can't trust it.

Try as I might to be totally balanced, this is just my representation of scientific news stories and peer-reviewed work.

I suppose what I'm saying is that my blog, like all other blogs, is not a replacement for peer-reviewed literature and the blogosphere is not an alternative to peer-reviewed scientific journals.

As a scientist, I recognise that the peer-review system works. Of course, there are problems with it and a few high-profile cases where it seems to have failed us, but overall it has stood the test of time. The British Government has recently announced a review of peer-review, but I would be confident that it will be shown to be the best method at our disposal to verify scientific findings.

Unfortunately, it would seem that some commentators feel that peer-review is definitely old hat and that a new system is needed. Of course, I'm talking about James Delingpole.

In a recent interview with Paul Nurse, for the BBC programme Horizon, Delingpole argued for the use of what he called 'peer-to-peer' review.

As you'll see from the video clip of the interview below, Nurse first made an analogy between accepting the consensus scientific viewpoint on the treatment of cancer and accepting the consensus scientific view of climate change. Writing in The Telegraph, Delingpole, a well known climate change sceptic, subsequently described this analogy as "shabby, dishonest and patently false".

"The consensus on climate change; and the consensus on medical care", says Delingpole, "bear no similarity whatsoever". You can judge for yourself whether the analogy  makes sense or not.

Having been flummoxed by Nurse's astute line of reasoning, he was subsequently asked about his use (or not) of peer-reviewed climate change literature.

"One of the main things to have emerged from the climategate emails was that the peer-review process has been, perhaps irredeemably corrupted" replied Delingpole.

"What I believe in a process called peer-to-peer review. The internet is changing everything. What it means is that ideas which were previously only able to be circultated in the seats of academe, in papers read by a few people can now be instantly read on the internet and assessed by thousands and thousands of other scientists; people of scientific backgrounds and people like me who haven't got scientific backgrounds but are interested."

What he's talking about of course is the blogosphere. Now, as keen as I am on this whole blogging lark, I do not believe that the ability to switch on a computer and type entitles anyone (including myself) to begin to interpret scientific data for which we are wholly unqualified. Sure, we can have opinions and ideas about the findings but, as the old adage goes,"we are not entitled to our own facts".

Delingpole however seems to have no time to even begin to interpret the data correctly:

"It is not my job to sit down and read peer-reviewed papers because  I simply haven't got the time, I haven't  the scientific expertise. What I rely on is people who have got the time and the expertise to do it and write about it  and interpret it. I am an interpreter of interpretations."

All well and good, and it's to his credit I suppose, that he admits that his opinions are not based on the real, original data. However, if he is to interpret the data (or the interpretations of the data... you know what I mean) then he must interpret all of the data and that means the overwhelming volume of research that points  to a global warming phenomenon caused by human interventions.

I may blog, but blogs are not real science. You can trust me on that!

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