Our new bioinformatics and molecular evolution lab website is now up and running and you can see it at http://bioinf.nuim.ie

Just posted this on ResearchGate: http://www.researchgate.net/profile/James_Mcinerney/blog/29011_Goods-thinking_versus_Tree-thinking

Linus Pauling was one of the most curious of Nobel prize winners.  Along with Marie Curie he is one of only two people to have won Nobel prizes in two different categories - in Pauling’s case, these were Chemistry and Peace.  He is the only person, so far, to have won two unshared Nobel prizes.  In my opinion, he might have won a third or even a fourth Nobel.  In a short note to the Journal Nature, Jim Lake, whom I have published with in the past, wrote about Pauling’s thoughts on why he was not the person who discovered the structure of DNA. Also, I feel that he might have won a prize for his work on protein structures.

He was a pacifist, who campaigned tirelessly in his later years, against the development of nuclear technology.  When he was awarded his second Nobel prize, he was under such strong suspicion as a consequence of his political activism and the US government denied him a passport in 1952 when he wanted to go to speak at a meeting in London.  they were sort-of forced to give him one in 1954 when he wanted to…pick up his first Nobel prize.

His second Nobel prize was awarded in 1963 on the day that John F. Kennedy signed into law the partial ban on nuclear testing along with Nikita Krushchev.  This was a ban on above-ground testing of nuclear weapons because Pauling had been instrumental in showing that strontium got into children’s teeth as a consequence of nuclear testing.  The citation for his second Nobel prize contained the sentence: “Linus Carl Pauling, who ever since 1946 has campaigned ceaselessly, not only against nuclear weapons tests, not only against the spread of these armaments, not only against their very use, but against all warfare as a means of solving international conflicts.”

He had some kooky moments, like when he insisted that vitamin C could cure cancer and when he thought that people that carried a defective gene for sickle-cell disease should be tattoo’ed, but overall he tried to do good and in my area of research he was instrumental.  In 1965 he wrote a manuscript with Emile Zuckerkandl where they showed that we could reconstruct the evolutionary history of life on the planet by looking at the amino acid sequences of the proteins that these organisms contained.  In writing this manuscript they kick-started the field of molecular evolutionary studies.

Now and again a scientist comes along who was just as interesting away from science as they were as a a scientist.

Marie Curie surely fits this description.

She won her first Nobel prize along with her husband Pierre and Henri Becquerel in 1903 and this prize was in Physics.  Her second Nobel prize she won on her own and this was in chemistry seven years later in 1911.

Her daughter and son-in-law also won a shared Nobel prize in 1935.

So the extended family won five Nobel prizes, which is a bit wow.

Probably the most important piece of work that Marie Curie did was to show that Uranium emitted radiation, not as some kind of chemical reaction, but as some kind of direct energy from the molecules themselves.  She did this for her PhD and this was the basis for her first Nobel prize.

Marie Curie was not only, arguably, the worlds greatest scientist of her time, but she also contributed to the development of her home country, Poland, setting up an oncology institute in Warsaw, which was directed by her sister and she also was a notable contributor to the war effort in the first world war.

Pierre, her husband died in a traffic accident in 1906 and she was apparently devastated after his death and she wrote that from that point on she became incurably lonely.

1911 was a particularly eventful year in Marie Curie’s life.  In 1910-1911 she had an affair with a the physicist Paul Langevin who was estranged from his wife, but at that time it caused somewhat of a scandal and was used against Marie Curie. The press printed speculation that she was Jewish - which was deliberately aimed at a public that tended toward xenophobia- and because she was older than Langevin, they called her a home-wrecker and more.  She won her second Nobel prize that year, she persuaded the French government to build the Marie Curie institute in Paris.

However, in that very year, when she won her second Nobel prize, she was not elected to the French Academy of Sciences.  She would have been the first woman if she was elected, but the academy maintained its prejudice against women and instead elected a scientist that was involved with the invention of the telegraph.  It would be another 50 years before the French academy elected a woman as a member.  Interestingly the woman they elected was a doctoral student of Marie Curie.

When Marie Curie worked on radiation, she had no idea of the ill-effects of this work.  She carried radioactive substances around with her, kept them in her desk drawer and never knew the danger.  She died of cancer and indeed today so much of her personal items are so radioactive that they are kept in lead-lined boxes.  Her cookbook is radioactive.

She is now interred in the Pantheon in Paris, along with her husband Pierre.  She is the first woman to have been interred in the Pantheon on her own merits.

It’s quite a shame that we don’t know more scientists by name.  However, unlike pop-stars, politicians and even economists, we know very few scientists by name.  The ones we tend to know are the ones that massively changed how we view the world.  Such is the extent of the contribution that must be made by a scientist before we actually get to remember their names.

We know Darwin, Einstein and Marie Curie.  Perhaps we know a few more.  Some might know Linus Pauling (the only person to be awarded two unshared Nobel prizes), but unless they write popular books (ala Dawkins, Hawking and so on), we usually don’t know who discovered what.

Even when we know their names, we often know very little apart from the fact that Darwin *somehow* came up with the theory of evolution and Einstein has a formula about light.  Marie Curie did something with radiation and it killed her.

This is a pity, but not surprising to be honest.  Often scientists find the whole process of science and discovery to be much more interesting than science communication and indeed often they are not the most fluent of communicators.  Often they simply don’t have the connections to get their message out there and nowadays scientists specialise so very much that it is unlikely that somebody will be able to hold an audience for very long with their tales of proteins that stick out of of membrane or whatever.

So, we don’t know a whole lot of scientists.

…and it is a pity ‘cos we are really interesting. ha ha.

I have just arrived back from the annual meeting of the Society for Molecular Biology and Evolution (SMBE 2011) in Kyoto, Japan.  This was a fantastic meeting with a huge number of speakers and posters.

Unfortunately, in large part due to the Tsunami in March of this year, the number of attended of the meeting was lower than expected, making the organisation somewhat difficult for the organisers, though they did a sterling job, given the circumstances.  All the plenary lectures went ahead, the student sessions, everything.  I enjoyed the meeting enormously and met everybody that I was hoping to meet.

The main reason for me going to the meeting was because on the first day, at the society’s council meeting, I had to present the organisational details for next year’s meeting.  This is because next year’s meeting is in Dublin, Ireland.

We are going to hold the meeting from June 23 to June 26 in the Convention Centre Dublin.  We have made plans for up to 1, 300 delegates to attend the meeting and we hope to have at least four parallel sessions going at any given time.

This is proving - as expected - to be an organisational juggernaut, but it is very interesting to see how everything happens.  For instance, the ‘discounts’ you can negotiate from various providers is enormous.  You can easily get things for less than 50% of what you are quoted for the first time out.  I’ve learned my lesson in that respect.

We made the very sensible decision of taking a professional conference organiser on board in order to make the meeting happen smoothly.  Our organiser is MCI Dublin.  So far, I can see that they really know their stuff and it is great to have such expertise. Initially, I thought this might be overkill, but now I know it is not.  I might be brave enough to try to organise a meeting of a couple of hundred people, but for more than 3-400, I think it would be too much - for me at least.  I have been talking with the society about the possibility that they would put out to tender for a global conference partner, with, say, a 3-5 year contract.  This would ensure continuity of the knowledge of how to run the meetings, one company would already have a mailing list of previous attendees, would know the council and how the society is run and would probably be in a very good place after the first year to simply roll out the conference year after year.

Anyway, we are now in the run-up to SMBE 2012 and I hope to post here from time to time on how progress is going.

So, the first hundred days are upon us and indeed it would not be possible to imagine a more difficult time to come into government.  The larger party - Fine Gael - campaigned on the basis of a “five-point plan”, so I thought I would review this plan and see how the election promises match the outcome.

 1. Politicians would lead the way and there would be reform of politics.

This one gets a 50:50 response from me.  On the one hand, the government is still making noises about reform, including reforming the Seanad.  We haven’t seen any concrete proposals yet, but the noises are still being made.  On the issue of politicians leading the way, the outcome is very different.  We have seen a long line of ‘cute-hoor’ moves by politicians in our new government, including Ciaran Cannon, who employed is wife as his secretary and his brother as his driver.  Others include Shane MacEntee, who employs his daughter and sister on the taxpayer’s dime, and Arthur Spring has employed his brother to be his secretary.  More details are here. Are these really the most competent people?  It almost looks like the new government got rid of the Garda ministerial drivers so that they could give the jobs to party loyalists.

Verdict: 3/10

2. Smaller, Better government, Services you need are prioritized over back-room waste.

Hard to judge this one yet.  This really take a bit of time.  Yesterday there was an announcement that the “Croke Park” deal had resulted in €600 Million in savings in its first year.  Mostly through retirements and no new recruitment, but also changes to work practices. In my experience so far, the Croke Park deal is a very blunt instrument for change, just randomly forcing change across the board.  I haven’t seen the new proposals to make it more targeted, though, of course, I might have missed them.  What is needed on this issue is a scalpel, not a sledgehammer.

Verdict: too early to say.

 3. A completely new health system

The first thing that James Reilly did was to abolish the board of the HSE, though arguably, this was on the cards in any case.  In terms of the health service, it looks so far like a lot of bluster, but again, it is very early to say whether we are on a trajectory towards fixing it.  What is clear is that Mary Harney wasn’t able for the job, so the fairest thing is to wait for at least the first 300 days.  However, if we are not seeing changes this winter, with waiting lists abolished, then this will have been an empty promise too.

Verdict: A little done, more to do.

 4. Fixing the deficit, jobs protected by no income tax increases and cutting waste.

The deficit is not fixed, nor are we moving towards it.  Enda Kenny got roasted, according to the Economist when he turned up in Brussels with the wrong attitude.  The bond holders have drawn down their money, week-in, week-out with no chance in the policy of the last government to push us deeper and deeper into debt.  “Burning” bondholders now is almost a useless enterprise, burning them 100 days ago might have paid some dividends.  There is no increase in job protection and I have no doubt that because of the direction we have taken with the bond holders, we are about to get hit with income tax hikes. As for “Cutting waste”, the waste has not been defined.  What were they talking about? Was that just something that looked good on an election poster?

Verdict: 1/10

 5. Jobs - protecting and creating jobs

Where is the job creation initiative?  If this was already planned during the government’s 15 years in opposition, then surely they would have burst out of the starting blocks with their jobs initiatives, no?   The only thing that has been done is that the wages of the lowest-paid people in Ireland are going to be hit, in order to create jobs.  It looks like today, there is a plan to hit social welfare - which will obviously be necessary because now it would be more beneficial to be on the dole, rather than to work in a low-paid job. Protecting and creating jobs?  If there is a plan, I haven’t seen it.

Verdict: 0/10

Enda Kenny still has the goodwill of the people.  This is important for us all that he does.  He still has lee-way and he has political capital that he can spend.  He can make tough decisions for a few more weeks without any serious adverse effects on his leadership.  However, he has to make some moves soon.  The government seems to me to be somehow moribund, terrified of action, going along with everything without doing much really.  Michael Noonan is going to Europe today with a proposal to make some bondholders take a discount on their bonds.  This is very little and very late, though I think Noonan has some measure of what the job entails.

This first 100 days has been filled with revelations of cronyism and has exploded the myth that Fianna Fail are the only morally corrupt party in the state - they are all at it.  It has been filled with revelations that being in opposition and being agin’ everything is much easier than being in office and having to do positive things.  Protest is easy, government is difficult.

It seems that the fees for third level institutions are to be increased by €500 - an issue that saw 40,000 students march in protest last year when it was suggested.  When I raised the issue of student fees with a particular Student’s Union president who campaigned vociferously last year against fee increases, he shrugged his shoulders and said about the new minister for Education, “I guess his hands are tied”.  The action, it seems, is only reprehensible when a particular politician takes that action, but it is all right when a different one takes the action.  This is not acceptable to me.

So, 100 days and plenty of activity without action.  Lots of active inaction, politicking and press releases, but Ireland is not in a significantly better place today than it was 100 days ago.

Overall verdict: 3/10.

As a nice digression, a bit of comedy:

It is becoming more commonplace - every few months we are hearing about a new bacterium or virus that is threatening humanity.  They seem to pop up all the time with scientists appearing on TV looking worried, with politicians deciding to impose restrictions on the movement of humans or food or animals or whatever.

It seems that it is happening more and more frequently and people are asking “why?”

There are numerous reasons why these bugs are appearing on our radar screens, but I will address one.

A process that has been going on since the dawn of time is the process of Horizontal Gene Transfer.  This means that in bacteria and viruses and maybe some other small creatures we see that genes ‘jump’ from one species or strain to another.

There are about 5 different mechanisms that facilitate the movement of these genes and it would be a bit tedious to list them here and try to explain the processes, so suffice it to say that acquisition of a gene by a bacterium is generally not a problem.

For us, however, this is a real problem and in the future it is likely to be much more of a problem, particularly when the genes involved are capable of turning a normally innocuous bacterium into a killer or when the genes make the bacterium resistant to a particular antibiotic.

A  bacterium has anywhere from about 500 to 10,000 genes and each gene needs to be replicated when a bacterium divides into two daughter cells.  So, this takes energy.  Not a lot of energy, but some energy nonetheless.  Therefore, bacteria don’t take on these new genes unless it is a good idea.  Unless it confers what we call a “selective advantage” on the bug.  This is classical Darwinian selection for ‘fitter’ kinds of organisms.

In normal, antibiotic-free circumstances the ’slimmed down’ bacterium is fitter than the one that is carrying the resistance genes.  In the absence of antibiotics, the bug without the antibiotic-resistant gene is expected to do better.  It won’t have to use energy replicating this gene that is not doing anything.  The antibiotic sensitive bacterium wins. As long as we don’t use antibiotics unnecessarily, we should be fine.

However…

For the past 75 years we have been doling out antibiotics for almost everything, killing all the antibiotic sensitive bacteria.  In Darwinian terms - the drug-sensitive bacteria are not the fittest in this environment.  This clears the road for the antibiotic resistant bacteria.  They are the winners, they will increase in numbers and now, without frontline antibiotics to deal with them, humans are exposed.

The lesson is not new - only use antibiotics when you really, really need them.  I remember a time when it was common for doctors to hand out antibiotics when people had the flu - apparently it was in case you got a secondary infection.  The suspicion is that you would be very reluctant to pay your 70 Euro for your doctor to send you home telling you to take a Lem-Sip.  Therefore, in order to look like they were treating you, they prescribed antibiotics.  I understand it is still a huge problem in parts of the developing world.

So, while we are using lots of antibiotics, clearing the path for the resistant ones, we should not be surprised to find multi-drug resistant strains of bacteria emerging and very, very soon most pathogens will be antibiotic resistant.

So, my advice….try to fight infection on your own and only take antibiotics when you really cannot deal with the infection.  However, don’t go overboard with this advice - don’t leave it too late either.

In the past couple of weeks there have been reports of a new deadly strain of E. coli that has caused more than 2,000 illnesses in Europe and it seems it has now moved to the US.

I have a few things to say about it.

First of all, it is a pretty regular E. coli.  It hasn’t evolved as a result of dodgy food practices or because of genetic modification by scientists.  It is the latest in a long line of bacteria that have evolved by the acquisition of genes from another bacterium - the process is known as “horizontal gene transfer” and it is as old as life itself.

Being a regular E. coli it is sensitive to cooking and so properly cooked food will not present a hazard to people.

Raw food - salads and so forth - should be washed carefully, thoroughly, in clean water and then they should be fine too.

Global travel will mean that this bug will spread, but that is what all bugs do these days.

Should we be worried? We should be careful with food, but this is a rule always.  The problem with the media is that if you run with a story like this, you are ‘hyping’ it, if you don’t you are hiding it and the papers/TV/radio have strict limits on the length of any report, so they don’t often get to present a detailed account of the issue.

The genome sequence of this bacterium (that is to say the entire DNA sequence) is now known.  This genome has been sequenced in at least two places, but the one that is better known is the Beijing Genomics Institute (BGI) with whom we are working on an entirely different project.

From the reports, the genome of this bacterium is about 93% identical to another known E. coli, but with some crucial differences.  My understanding is that these differences relate to the bacterium’s ability to stick to human cells.  This difference is important for disease.

The genome sequence has also revealed that the bacterium is carrying some genes that make it resistant to about three classes of antibiotics.  But we now know which antibiotics are likely to be successful, so these others can be used instead.

In addition, because we know the genome sequence, we now have a very quick test (we can ‘probe’ a specimen to ask whether it has DNA sequences on its surface that are ‘diagnostic’ of this bacterium) and we might be able to trace the origin of the outbreak with this test.

Horizontal Gene Transfer is something we are really only appreciating now as a big driving force in the evolution of bacteria.  Antibiotic resistance is largely driven by horizontal gene transfer.  New pathogenic strains are frequently arising as a consequence of horizontal gene transfer.  Some bacteria do it more than others.  The reason for only having partially effective vaccines against all the serogroups of bacterium that causes meningitis is because these bacteria change all the time as a consequence of horizontal gene transfer.

My research group at NUI Maynooth works on this area and has been working on HGT for about 10 years.

In 2012 I, along with three other Irish academics will organise one of the largest molecular evolution conferences in the world that year.  There will probably only be one other meeting that is bigger than it in that year.

We will bring 1,300 delegates to the conference and probably about 200 of them will bring a partner.

So, 1,500 people will come here for about 5 days and approximately half of these will stay for another week for a short holiday.

This will fill approximately 12,500 bed-nights (if indeed that is a unit or measurement) in Irish hotels in that year. They will eat 15,000-30,000 sandwiches, eat 15,000 dinners and breakfasts.  They will buy magazines, newspapers and souvenirs, they will go the Guinness storehouse, they will take bus, train and aeroplane trips, they will visit the Aran island, the cliffs of Moher, Bantry, Dingle and Donegal.

The benefit to us academics in Ireland is enormous and long-lasting.  The goodwill we will generate by doing a good job is not really measurable, but it certainly will be a major positive.

The value to Ireland is also massive.

This conference alone is worth more to the Irish exchequer than my lifetime salary costs the exchequer.

A conservative estimate  would say that this is worth about 3 million Euro to Ireland.

We need to do more of this kind of thing.

There is a lot of talk about bringing students into Ireland for third level education and indeed this might make sense, if we improve the supports within the university system.

However, something that is much simpler is to step up the number of international conference we hold in Ireland each year.

We got huge amounts of funding from SFI over the past decade.  We have an excellent international profile in lots of diverse areas of Science, Law, Economics, etc etc.  Why not cash in on this immediately?

We can hold big conferences in the CCD, RDS and CityWest (others?).  We have struggling conference venues in hotels all over the country.  Let’s make use of them.  We have lecture theatres that are empty in the summer, why not make use of them?

This is a relatively simple thing to do.  We could easily hold conferences that would be worth €500 Million each year (150 big conferences would do it, there are 500 professors in the country).  In one decade we would have returned every penny we ever got from the exchequer many times over and on top of that the taxpayer would have gotten graduates, teaching, patents, tech-transfer and reputational benefit.

What is needed is some kind of seed funding (S.F.I. provide some in the area of Science funding, so this is a good start) and for academics to be given the time to dedicate to organising these events.  It is not so onerous when you have excellent professional conference organisers in the country (we are using MCI).

Conferences - use our reputations!