Posts Tagged ‘scientific thinking’

Trinity College Institute of Neuroscience Strategic Plan 2010-2016

November 11, 2010 Leave a comment

Blogging has been light recently because of the usual term-time stuff. However, we have launched our Institute of Neuroscience Strategic Plan (also available via google docs).

See here for the Trinity press release and TCIN Strategic Plan Nov 2010 Final for the summary presentation pdf.

The graphics are fantastic, and the plan itself is short and sweet.

A quote:

Our animating ethos rests on the belief that major and fundamental research problems are best solved by combining research strengths across disciplines and levels of analysis.

Combining our strengths in this way will allow us to deliver major scientific discoveries of great consequence for human health, welfare and knowledge.

Table of Contents:

  1. Why Explore the Brain? [Our short, simple answer: ‘Understanding the structure and functions of our brains brings us a good way along the path of understanding ourselves as humans. Progress in understanding the nervous system materially benefits human health, welfare and knowledge.‘]
  2. Trinity College Institute of Neuroscience Mission
  3. Transformative Neuroscience
  4. Context
  5. Trinity College Institute of Neuroscience Today
  6. Trinity College Institute of Neuroscience Tomorrow
  7. Research Focus 1: Synapses, Cognition and Behaviour
  8. Research Focus 2: Neuropsychiatry and Neurodevelopmental Disorders
  9. Research Focus 3: Neurodegeneration, Neuroprotection and Neuroplasticity
  10. Platform Technologies: Imaging and Neural Engineering
  11. Innovation
  12. Education
  13. Contribution to Society and Outreach
  14. Future Opportunities
  15. Measuring Impact: Hard and Soft Metrics
  16. Final Thoughts

Read it!

Irish science blogs – from

September 29, 2010 Leave a comment

Irish science blogs.


Irish Science Blogs
Published 29 September 2010

There are lots of Irish science blogs nowadays where you can keep up with what’s happening in the world of science and find out what issues people are discussing.

These  bloggers range from scientists and science teachers to members of the public who have an interest in science.

To give you a flavour of what’s out there, have a look at these ones we’ve come across…

Antimatter, by physics lecturer and Science Ambassador Cormac O’Raifeartaigh

Chris Horn, leading Irish electronics engineer, entrepreneur and STEM policy expert

Communicate Science, by our Science Ambassador Eoin Lettice

The Frog Blog – St Columba’s College Science blog

Irish Science – this is by a group of contributors

James McInerney, evolutionary biologist

Karlin Lillington, technology journalist

Mary Mulvihill, science journalist

Michael Seery, lecturer in physical chemistry (his blog is called “Is This Going To Be On The Exam?”)

Science Communication Review by Diarmaid Mac Mathúna

The Science Gallery blog

Science Line by science journalist Cormac Sheridan

Science Spinning, by Seán Duke

The Strange Quark by Marie Boran

TeachNet Learning Blog

Think For Yourself by physics teacher Noel Cunningham

Using ICT in Further Education by Patricia Donaghy, ICT teacher

Last but not least, don’t forget to check out our own blog at

Government Announces New Research Funding Partnership with the Wellcome Trust

September 29, 2010 Leave a comment

A press release from SFI:

Ministers welcome joint funding deal boost for pioneering biomedical research

Wednesday, September 29th 2010: Minister for Health and Children, Mary Harney T.D., and Minister for Labour Affairs and Public Service Transformation, Dara Calleary T.D., have welcomed the announcement today of a partnership agreement between Science Foundation Ireland (SFI) and the Health Research Board (HRB), with the Wellcome Trust, a global charitable foundation based in the UK.

The new SFI-HRB-Wellcome Trust Biomedical Research Partnership will mean that the prestigious Wellcome Trust will jointly fund biomedical researchers in Ireland with Science Foundation Ireland and the Health Research Board.

Minister for Health and Children, Mary Harney T.D. described the forging of the new arrangement as “a significant occasion for health research in Ireland”. She added “Vibrant health research is critical to how we generate new ways to care for patients, advance the delivery of our health services, and contribute to our economic development.  This agreement will add to the international standing of Ireland in health research and increase our attractiveness as a location for research and development in biomedical and lifesciences.  Today’s strategic partnership with the Wellcome Trust represents a significant boost for the entire spectrum of Irish health research.

Speaking at the announcement of the new partnership, Sir Mark Walport, Director of the Wellcome Trust, said: “We are delighted to enter into this partnership with Science Foundation Ireland and the Health Research Board. By working together, our joint funding will support the best scientists and clinical researchers in Ireland, ensuring that biomedicine in the country remains globally competitive.”

Commenting on the importance of the agreement, Minister for Labour Affairs & Public Service Transformation, Dara Calleary T.D., said “For Ireland’s smart economy to properly manifest itself in our day-to-day lives, excellence in science, health and engineering R&D must be identified and given every opportunity to progress and prosper. The signing of this collaborative funding deal is a major endorsement of Ireland’s research potential, and will greatly assist its connectivity with the international research community and, particularly, its engagement with the commercial sector, both here and abroad.”

The announcement of the agreement was also attended by Prof Pat Fottrell, Chairperson, Science Foundation Ireland, Dr Stephen Simpson, Director of Life Sciences at Science Foundation and Mr Enda Connolly, CEO of the Health Research Board.

About the Wellcome Trust

The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. It supports the brightest minds in biomedical research and the medical humanities. The Trust’s breadth of support includes public engagement, education and the application of research to improve health. It is independent of both political and commercial interests.

The Frog Blog: Creating a Blogging Network for Irish Science Communicators

September 22, 2010 1 comment

The Frog Blog: Creating a Blogging Network for Irish Science Communicators.

Now here’s a great idea from The Frog Blog [blog post reproduced in full]:

Creating a Blogging Network for Irish Science Communicators

Blogging, for me, is an opportunity to reveal the wonders of the natural world to all age groups and bring to light the vast multiplicity that exists in the world of science, nature, technology and engineering. It is about promoting critical thinking and questioning skills, informing and enthusing and, specifically as a teacher, it’s about dispelling the view of science as stagnant and dormant, as portrayed by our inadequate science curricula. Science is an ever evolving field, where individuals seek the truth and aim to solve our society and world problems through investigation, experimentation and exploration.
Science is now more important to the Irish public than ever before, as our government finally begins to see the value of scientific research in the face of economic meltdown. Over the coming years and decades, our government aims to create a “smart economy”, with Irish people working in science, technology, engineering and other cutting edge fields. Ireland’s young people are now being encouraged to study science and related courses in university and, for this reason, it is extremely important that good science communication be available to the Irish public.
Ireland is awash with excellent science communicators. Established science bloggers like Eoin Lettice, Mary Mulvihill, Shane O’Meara*, Sean Duke, James McInerney, Cormac O’Raifeartaigh, Marie Boran, Cormac Sheridan, Diarmaid Mac Mathúna, Noel Cunningham and Michael Seery do an excellent job promoting their fields. The Irish Times science team, which includes Dick Ahlstrom, Claire O’Connell and William Reville, are the sole national media organisation to have a devoted science section. The science message is getting out there, but I ask one question, is its message reaching a wide enough audience?
Not meaning to offend anyone, science blogs have a specific followership – generally those already with an interest in science – and every blogger / writer wants to improve their readership figures. Our national broadcaster, RTÉ, is doing little to promote the sciences to a general audience (unlike the BBC) and it is being left to science blogs and a few other publications (like the Irish Times and Science Spin) to enthuse, inform and promote the work of Irish researchers. Of course, I must mention the brilliant work of Discover Science and Engineering and the wonderful Science Gallery in the elevation of science communication in Ireland too.
What I wish to propose is this – a central network of Irish science bloggers similar in structure to the newly launched Guardian Science Blogs. Such a network would provide a medium for the provision of science news and stories relevant to the Irish public. All that would be required are five or six principal writers, each with a specific remit, contributing one or two accessible pieces per week. Of course, there should also be scope for guest bloggers too, providing the Irish public with a vibrant platform for learning, debate and entertainment.
The most effective way to introduce such a network would be through an already well established and highly trafficked platform – ideally a national newspaper like the Irish Times, Irish Independent etc. The Irish Times immediately comes to my mind, as it is the only Irish newspaper and media website with a dedicated science section.
I don’t mean to sound preachy on this – I am just a lowly science teacher after all – so I would like to invite anyone to comment on the idea and provide suggestions for its implementation, should consensus be established on the value of such a network (Please be aware that the Frog Blog is aimed at science enthusiasts of all ages so comments are moderated). Ireland needs good science communication right now and, I believe, it is time for science communicators to work together and unite in the promotion of science.

[* It’s O’Mara! ;-)]

Evolution and Minister Lenihan

September 14, 2010 Leave a comment

There’ s been lots of comment about the welcome decision of Minister Lenihan’s to recuse himself (or be recused?) of further involvement in the launch of a book by a constituent of his that purports in some grandiose terms to disconfirm the theory of  evolution (Darwin’s one – not some of the other ones!). The story has spread widely – PZ Myers of Pharyngula (one of the most widely read science blogs on the planet) even carries the story.

I won’t link to the website of said constituent (do a search; a link is simply not appropriate here), but reading it and the sample material available is a remarkable experience. The theory of evolution by natural selection as presented bears little relation to anything that you might find in a contemporary textbook or indeed in the J Theor Biol (or wherever).

So what is the theory of evolution? Here is a simple and accessible statement by a major leader in the field:

RC Lewontin: ‘Darwinism is a population-based theory consisting of three claims. First, there is variation in some characteristics among individuals in a population. Second, that variation is heritable. That is, offspring tend to resemble their biological parents more than they do unrelated individuals. In modern Darwinism the mechanism of that inheritance is information about development that is contained in the genes that are passed from parent to offspring. Third, there are different survival and reproduction rates among individuals carrying different variants of a characteristic, depending on the environment inhabited by the carriers. That is the principle of natural selection. The consequence of differential reproduction of individuals with different inherited variants is that the population becomes richer over generations in some forms and poorer in others. The population evolves.’

This is a pretty straightforward set of claims. The contemporary theory of evolution makes the following (empirically-testable) assumptions:

  • Long periods of geological time (~ a billion or so years for the current speciation evident on Earth);
  • Cumulative selection;
  • Genotypic variation;
  • A mechanism for inheritance;
  • Variation in the environment over time driving evolution – ‘selection-pressure’ and ‘resource-pressure’.

What empirical observation would prove evolution wrong? Flippantly but profoundly, J.B.S. Haldane (discussed on this blog recently), replied when asked what empirical evidence disprove evolution “fossil rabbits in the Precambrian era“.

Said constituent is apparently offering a monetary prize for anyone who can demonstrate ‘biochemical evolution’. I’m not certain what this means, but I guess the famous citric acid metabolism experiments (see here for a wiki account) might entitle Richard Lenski to the prize. I presume the prize is offered in the belief that no-one can claim it, but I could be wrong…

From the wiki article above (but read the cited PNAS and other papers cited here – they are available for download):

The E. coli long-term evolution experiment is an ongoing study in experimental evolution led by Richard Lenski that has been tracking genetic changes in 12 initially nearly identical populations of asexual Escherichia coli bacteria since February 24, 1988.The populations reached the milestone of 50,000 generations on early 2010.

Since the experiment’s inception, Lenski and his colleagues have reported a wide array of genetic changes; some evolutionary adaptations have occurred in all 12 populations, while others have only appeared in one or a few populations. One particularly striking adaption was the evolution of a strain of E. coli that was able to grow on citric acid in the growth media.

This should qualify shouldn’t it?

[Update: The Irish Times story is worth reading; it notes the existence of the prize for ‘…prov[ing] evolution at a biochemical level’.]

Some Nerve – The Scientist – Magazine of the Life Sciences – An interview and profile of Rodolfo Llinas

September 14, 2010 Leave a comment

Some Nerve – The Scientist – Magazine of the Life Sciences.

Llinas is one of the great integrative neurophysiologists – this is a fantastic interview and profile.

A quote:

“My interest in science came from basic curiosity,” says Rodolfo Llinás of the New York University School of Medicine. “My interest in the nervous system came from my grandfather.” As a precocious preschooler, Llinás lived with his paterfamilias, a psychiatrist who ran his practice from home. There, the young boy encountered individuals with a cavalcade of psychiatric and neurological conditions, including one patient who experienced an epileptic seizure in the waiting room.

“I remember being amazed,” says Llinás, who asked his grandfather why the man would behave that way. “‘He didn’t want to do it. He couldn’t help it. His brain did it,’” his grandfather explained. For Llinás, the idea that the brain had a mind of its own was eye opening. “And the more I talked to the old man about these things,” he says, “the more I came to see that everything we do, everything we understand, everything we are, is focused on the brain.”

Read more: Some Nerve – The Scientist – Magazine of the Life Sciences

Titans of science: David Attenborough meets Richard Dawkins | Science | The Guardian

September 13, 2010 Leave a comment

Titans of science: David Attenborough meets Richard Dawkins | Science | The Guardian.

A wonderful conversation.

A few quotes:

What is the one bit of science from your field that you think everyone should know?
David Attenborough: The unity of life.

Richard Dawkins: The unity of life that comes about through evolution, since we’re all descended from a single common ancestor. It’s almost too good to be true, that on one planet this extraordinary complexity of life should have come about by what is pretty much an intelligible process. And we’re the only species capable of understanding it.


What is the most difficult ethical dilemma facing science today?
DA: How far do you go to preserve individual human life?

RD: That’s a good one, yes.

DA: I mean, what are we to do with the NHS? How can you put a value in pounds, shillings and pence on an individual’s life? There was a case with a bowel cancer drug – if you gave that drug, which costs several thousand pounds, it continued life for six weeks on. How can you make that decision?

Self-experimentation – Scientists treating themselve as guinea pigs [from Oscillatory Thoughts: Sir Henry Head’s self-experimentation]

September 12, 2010 1 comment

Oscillatory Thoughts: Sir Henry Head’s self-experimentation: a great post on a long-standing but little known tradition in science – especially physiology and psychology – experimenting on one’s self, usually to do unpleasant and excruciating things that might not pass an ethics committee!

The great evolutionary theorist, JBS Haldane, was famous for this sort of thing. From a New Scientist story:

JBS Haldane’s smoking ear

One self-experimenter whose work had long-term personal consequences was the polymath JBS Haldane.

Haldane wanted to build on work done by his father, John Scott Haldane, on the physiology of working Navy divers in the early 20th century. But whereas Haldane senior restricted himself to observation and measurement, his son took a more direct approach, repeatedly putting himself in a decompression chamber to investigate the physiological effects of various levels of gases.

Haldane was motivated by concern for the welfare of sailors in disabled submarines, and his work led to a greatly improved understanding of nitrogen narcosis, as well as the safe use of various gases in breathing equipment. But he paid a high price, regularly experiencing seizures as a result of oxygen poisoning – one resulting in several crushed vertebrae.

He also suffered from burst eardrums, but he was sanguine about the damage. “The drum generally heals up,” he said, adding, “if a hole remains in it, although one is somewhat deaf, one can blow tobacco smoke out of the ear in question, which is a social accomplishment.”

From the blogpost cited at top:

Following in this fine scientific tradition is the brilliant and influential neurologist (not to mention appropriately named) Sir Henry Head. If that’s not a proper 1960s punny, alliterative, Stan Lee name for a neurologist, I don’t know what is. Anyway, the good Dr. Head published quite a ground-breaking article with his collaborator WHR Rivers in the journal Brain in 1908 titled A Human Experiment in Nerve Division. In this article, Head and Rivers sought to examine the course of recovery of somatosensation after peripheral nerve damage. It was known from observing patients with such damage that the touch senses often recover after peripheral nerve damage, but because the patients weren’t properly trained, they couldn’t give an adequate account of their own recovery. As they say:

“It soon became obvious that many observed facts would remain inexplicable without experimentation carried out more carefully and for a longer period than was possible with a patient, however willing, whose ultimate object in submitting himself to observation is the cure of his disease.”So Head’s solution? Cut open his arm and sever some nerves! Dr. Head enlisted the assistance of another doctor to surgically sever some of the peripheral nerves in his left arm and hand.

I recall reading a case report by the late (and great) OJ Grusser where he injected the dissociative anaesthetic and glutamergic antagonist ketamine into his own eyeball to study its effects on optokinetic nystagmus (the tracking of moving objects when the head is stationary). The ketamine would inactivate transmission in the extra-ocular muscles, reducing reflexive tracking eye movements to moving objects. (I can’t locate the reference at the moment – my recollection is that it was in a book chapter). Not an experiment to be undertaken lightly!

Loss aversion and ‘thinking’ about the house price collapse (in Ireland and further afield)

September 4, 2010 Leave a comment

There has been a dramatic collapse in house prices in many parts of the world, including Ireland, which has seen prices come down by 40% or so on average since the peak a few years ago (and more to come, according to some economists). The market is now very slow-moving, and probably as bad as it ever has been. And given past patterns, will probably take a decade to recover. Jonah Lehrer has a fantastic post on the pervasive phenomenon of loss aversion in human cognition which must underpin at least some of the problems in the market, because of the aversion and indeed pain caused by recognising losses quickly.

Key quote: “The pain of a loss was approximately twice as potent as the pleasure generated by a gain. Furthermore, our decisions seemed to be determined by these feelings. As Kahneman and Tversky put it, “In human decision making, losses loom larger than gains.”

[Blog reproduced in full]

The Real Estate Collapse By Jonah Lehrer

The news on the housing front is bleak and getting bleaker. The New York Times posts a graph that captures the trend:

Obviously, a stew of forces are at work here. There is the end of the federal tax credit, and the crappy employment news, and the shadow inventory of foreclosed homes. But I think the dismal housing data also reflects a systematic human bias: loss aversion. The phenomenon was first identified by Daniel Kahneman and Amos Tversky in the mid-70s, after they gave their students at Hebrew University a simple survey asking them whether or not they’d accept a variety of different bets. The psychologists noticed that, when people were offered a gamble on the toss of a coin in which they might lose $20, they demanded an average payoff of at least $40 if they won. The pain of a loss was approximately twice as potent as the pleasure generated by a gain. Furthermore, our decisions seemed to be determined by these feelings. As Kahneman and Tversky put it, “In human decision making, losses loom larger than gains.”

Consider this scenario:

The U.S. is preparing for the outbreak of an unusual Asian disease, which is expected to kill 600 people. Two alternative programs to combat the disease have been proposed. Assume that the exact scientific estimates of the consequences of the programs are as follows: If program A is adopted, 200 people will be saved. If program B is adopted, there is a one-third probability that 600 people will be saved and a two-thirds probability that no people will be saved. Which of the two programs would you favor?

When this question was put to a large sample of physicians, 72 percent chose option A, the safe-and-sure strategy, and only 28 percent chose program B, the risky strategy. In other words, physicians would rather save a certain number of people for sure than risk the possibility that everyone might die. But what about this scenario:

The U.S. is preparing for the outbreak of an unusual Asian disease, which is expected to kill 600 people. Two alternative programs to combat the disease have been proposed. Assume that the exact scientific estimates of the consequences of the programs are as follows: If program C is adopted, 400 people will die. If program D is adopted, there is a one-third probability that nobody will dies and a two-thirds probability that 600 people will die. Which of the two programs would you favor?

When the scenario was described in terms of deaths instead of survivors, physicians reversed their previous decision. Only 22 percent voted for option C, while 78 percent of them opted for option D, the risky strategy. Most doctors were now acting just like Frank: they were rejecting a guaranteed gain in order to partake in a questionable gamble.

Of course, this is a ridiculous shift in preference. The two different questions examine identical dilemmas; saving one third of the population is the same as losing two thirds. And yet, doctors reacted very differently depending on how the question was framed. When the possible outcomes were stated in terms of deaths – this is the “loss frame” – physicians were suddenly eager to take chances. They were so determined to avoid any alternative associated with a loss that they were willing to risk losing everything.

The same irrational quirk is now playing out in the U.S. housing market. Look, for instance, a 2001 paper by the economists Christopher Mayer and  David Genesove. They studied the Boston condominium market of the early 1990s, which was one of the most spectacular real estate busts in recent decades. Between 1989 and 1992, Boston condo prices fell by nearly 40 percent. This meant that, for the vast majority of condo owners, they could only sell their home at a steep loss.

Classical economics assumes that people will adjust to the new reality. They’ll realize that the market has changed, and that they made a costly mistake. But that’s not what happened. In their paper, “Loss Aversion and Seller Behavior: Evidence From the Housing Market,” Mayer and Genesove found that, for essentially identical condos, people who had bought at the peak of the market (between 1989-1992) listed their properties for nearly 35 percent more than those who had bought after the collapse. Why? Because they couldn’t bear to take a loss.

The end result, of course, is that these overpriced properties just sat there, piling up like unwanted inventory. According to the economists, less than 25 percent of the properties bought during the condo bubble sold in less than 180 days.

I’d argue that the same thing is happening right now, except on a nationwide scale. The housing market will only recover when we get over our collective bias, and realize that home prices have fallen and aren’t coming back (at least not anytime soon). Our irrationality got us into this mess – we binged on credit cards and took out unreasonable loans and mistook a bubble for a boom – and the only way we’re going to get out of it is to see through a new set of irrational quirks, which prevent us from fully equilibrating to our new financial reality. Sometimes, the wisest thing to do is cut our losses and run.

More at Wired.

Latest from the Science Gallery – BIORHYTHM: MUSIC AND THE BODY

The latest exhibition from the Science Gallery – including a contribution from Ian Robertson, who blogs here occasionally.


Are you looking to turn up the music now that summer’s finally here? Keen to find out if there is a formula to create the perfect hit? Want to know what makes us dance?

BIORHYTHM, Science Gallery’s latest exhibition, will explore all of these questions and more in an interactive bonanza of unique sonic experiences, where curators include Professor Ian Robertson, from the Trinity College Institute of Neuroscience, musician Gavin Friday and composer Linda Buckley, featuring research by Professor Carol O’ Sullivan’s GV2 group amongst the many experiments and experiences into the sounds around us.

BIORHYTHM opens to the public on July 2nd and runs until October 1st and will feature exhibits ranging from a sonic bed to musical instruments that respond to your heartbeat. BIORHYTHM will be open Tuesday-Friday 12:00-20:00 and Saturday-Sunday 12:00-18:00.

Do you want to be the first to experience BIORHYTHM at Science Gallery? Why not join the exclusive VIP Preview on July 1st (19:00-21:00)

Explore the installations, chat to the artists and enjoy an evening of aural delights.  Tickets (€10) are available for the launch on

However, do you fancy supporting Science Gallery, get FREE into all previews, get priority booking, free WiFi and discounts in the cafe and shop?

Then join as a Science Gallery MEMBER+ today.

All staff and students at Trinity College can sign up for only €20/year (compared to €30 standard rate) = sign up in Gallery only and please remember to bring your TCD ID.

If you join before June 30th you will automatically be on the guest list for the BIORHYTHM launch on July 1st and you will be entered into a draw to join Science Gallery Crew at Electric Picnic!

We look forward to welcoming you to a musical summer at BIORHYTHM at Science Gallery!

Kind regards

Michael John Gorman

Director of Science Gallery