The symphony of science

I had written previously a post entitled the sound of science. So this is a video of the symphony of science, a musical project headed by John Boswell, designed to deliver scientific knowledge and philosophy in musical form. This video features noted scientists and thinkers, Carl Sagan, Bertrand Russell, Sam Harris, Michael Shermer, Lawrence Krauss, Carolyn Porco, Richard Dawkins, Richard Feynman, Phil Plait, and James Randi.
It is amazing what people make!!!



Lyrics (taken from a Guardian science blogpost):

Russell:
When you are studying any matter
Or considering any philosophy
Ask yourself only: what are the facts,
And what is the truth that the facts bear out

Sagan:
Science is more than a body of knowledge
It's a way of thinking
A way of skeptically interrogating the universe

If we are not able to ask skeptical questions
To be skeptical of those in authority
Then we're up for grabs

Shermer:
In all of science we're looking for a balance
between data and theory

Harris:
You don't have to delude yourself
With Iron age fairy tales

Porco:
The same spiritual fulfillment
That people find in religion
Can be found in science
By coming to know, if you will, the mind of God

Krauss:
The real world, as it actually is,
Is not evil, it's remarkable
And the way to understand the physical world
is to use science

Dawkins:
There is a new wave of reason
Sweeping across America, Britain, Europe, Australia
South America, the Middle East and Africa
There is a new wave of reason
Where superstition had a firm hold

Plait:
Teach a man to reason
And he'll think for a lifetime

Sagan:
Cosmology brings us face to face with the deepest mysteries
With questions that were once treated only
in religion and myth

The desire to be connected with the cosmos
Reflects a profound reality
But we are connected; not in the trivial ways
That Astrology promises, but in the deepest ways

Feynman:
I can't believe the special stories that have been made up
About our relationship to the universe at large
Look at what's out there; it isn't in proportion

Russell:
Never let yourself be diverted
By what you wish to believe
But look only and surely
At what are the facts

Randi:
Enjoy the fantasy, the fun, the stories
But make sure that there's a clear sharp line
Drawn on the floor
To do otherwise is to embrace madness

Consumer debt and mental health

[I recently applied for a job for which I had to produce a report on consumer debt and mental health. Even though I did not get the job, I did spent sometime to look over the issue so I am posting the report here.]

Consumer debt and mental health

Evidence has shown a clear association between consumer debt and mental health. Given the current financial crisis, extra measures are needed in order to deal with people affected. This note considers the published evidence on the above relationship, examines the current regulations and suggests what policies should be implemented in order to ensure that sensitive approaches are adopted for the benefit of the consumers, the health and social carers, and creditors.

Overview

·         There are clear links between consumer debt affecting mental health, and vice versa, even if the direction of causality has not been yet verified.

·         Given the current financial crisis, more people will fall in debt, leading to increased demand for mental health services.

·         Currently mental health and debt are treated as separate issues. Any links that exist between financial services and health and social sectors are underdeveloped, partly due to legal and regulatory barriers.

·         People need to be treated as “patients” and “bank customers” at the same time, so a co-ordinated cross-sector national approach is needed in order to mitigate the problems.

Definitions

• Consumer debt: debt incurred by an individual for personal, family or household purposes.
• Unsecured debt: if there is no collateral that is security for the debt. Most consumer debts are unsecured.
• Problematic consumer debt: when the individual is two or more consecutive payment behind
• Mental Health problem: anxiety and stress, depression, self-harm and suicidal thoughts, strain on personal relationships and self-esteem or social exclusion

Background

In 2008, UK households owed over £230 billion in unsecured consumer credit (see definitions box)[1], whereas the proportion of households reporting consumer unsecured debt as a financial burden in 2008 was the highest since 1995[2]. Given that being in debt can have a negative effect on one’s mental health and that those living with a mental health problem are more likely to fall into debt, a large percentage of the national consumer debt mentioned above is owed by people suffering from mental problems.

This percentage is likely to increase even further. Evidence suggests that large economic crises, such as the one we have been experiencing since 2008, have a detrimental effect on the mental health of a population. This is especially true for the vulnerable subgroups (e.g. those with pre-existing mental disorders, the unemployed and those of low socio-economic status)[3]. Many of these subgroups include people with little previous experience of coping with hardship and will thus be at greater risk of mental health problems, as compared to those ‘inured’ to financial insecurity⁵.

Scale of the problem

While there is a number of studies that have looked using different methodologies at the relationship between debt and mental health their majority has either treated all types of debt (mortgage, utilities, consumer, etc) as one, or did not specify what is meant by ‘debt’. For this reason, our evidence comes from 13 studies that have specifically investigated the relationship between consumer debt and mental health, or included consumer debt alongside other debt types[4].

These studies showed that consumer debt has negative effects on people’s mental health: those with consumer debt exhibited lower average levels of psychological well-being, higher levels of stress and depression. It was also found that those with mental health problems are more likely to be in debt. For example, a large UK survey by Mind showed that out of 924 individuals with mental health problems, half had arrears on credit/store cards, one in three on loan repayments and one-in-five on goods bought on hire purchase or mail-order[5].

Awareness

The link between debt and mental health has been recently recognised by a number of governmental departments. The New Horizons report on Mental Health mentioned that intervention to tackle social inequalities such as debt may be of benefit to individual mental health and recommended further research to be carried out around the issue[6]. However, no guidelines or recommendations were mentioned in the report. In addition, the department of Business Innovation and Skills has included specific reference to the issue of mental health in its Consumer White paper^[7] and the Office of Fair Trading has made repeated reference to the difficulties facing people with mental health problems. This recognition has been however for debt in general and not specifically for consumer debt.

A number of non-governmental initiatives have been undertaken in order to increase awareness of the relationship between debt and mental health of health and social care services, money advisors, financial services, government sectors, as well as people suffering from mental health problems. Similarly to the governmental reports above, all these initiatives did not concentrate on consumer debt, but some of them referred to it.

In 2006, the Royal College of Psychiatrists developed ‘Final Demand’ Booklet for health and social care professionals in order to help them respond quickly to the needs of patients who are suffering from mental health and financial problems[8]. They also created a standardised clinical information form, called ‘Debt and Mental Health Evidence Form’ (DMHEF) to be used by health and social care professionals in order to provide their patients with clear information on how to proceed. In 2007, the Money Advice Liaison Group (MALG) provided voluntary guidelines for money advisers and creditors to support the use of DMHEF[9]. More recently, MALG published “Good Practice Awareness Guidelines For Consumers with Mental Health Problems and Debt”[10]. Furthermore, a national campaign was carried out by Mind in 2008 which targeted the financial services as well as various government sectors.

Measures

Despite these efforts, links between financial institutions, money advisers and health and social care services are still severely underdeveloped. This means that the “health” and “debt” components of this issue are mostly addressed separately, making most strategies ineffective[11]. The strategy agreed by all parties is to foster and maintain a coordinated national programme in which all of financial, advice, health and social services would help individuals receive well organised and complementary support, regardless of entry point.

For such a programme to succeed the appropriate legal and organisational infrastructure needs to developed at all entry points, whether these are health and social care services, money advice or financial services. For example, creditors should be legally obliged to train their staff to encourage customer disclosure, especially since people with mental health problems tend to be reluctant to report it. Money advisers should be legally obliged to routinely provide referral services to clients that disclose a mental health problem for which they require support. Finally, all health and social care professionals should receive a basic ‘debt first aid training’, in order to know how to talk with patients about debt and how to refer to and support debt advisers.

In the mean time, new research needs to be commissioned and undertaken on the effects of consumer debt in particular. Not all consumer debt is problematic, research is needed to further understand when it becomes especially problematic, as well as the direction of causality between consumer debt and mental health. In these new studies there needs to be a consistency in the conceptualisation and measurement of debt (e.g. to differentiate consumer debt from other types of debt). Furthermore, a survey of the current practices of all types of financial services concerning costumers suffering from mental health problems, should be carried out.

---

Endnotes

[1] Bank of England (2008) “Lending to Individuals: December 2008” Bank of England statistical Release, London.

[2] Hellenbrandt. T and Young, G (2008) “The financial position of British households: evidence from the NMG research survey” Quarterly Bulletin (Bank of England) Q4: 384-392

[3] Zivin, K, Paczkowski, M and Galea, S (2010) Economic downturns and population mental health: research findings, gaps, challenges and priorities, Psychological Medicine 14:1-6

[4] Royal College of Psychiatrists (2009) “Debt and Mental health: What do we know? What should we do?” London http://www.rcpsych.ac.uk/pdf/Debt%20and%20mental%20health%20(lit%20review).pdf

[5] Mind (2008) “In the red: debt and mental health” http://www.mind.org.uk/assets/0000/9121/in_the_red.pdf

[6] HM Government (2009) “New Horizons: A shared vision for mental health” http://www.dh.gov.uk/en/Publicationsandstatistics/Publications/PublicationsPolicyAndGuidance/DH_109705

[7] Department of Business Innovation and Skills(2009)  “A better deal for consumers: delivering real help now and change for the future [Consumer white paper]” http://berr.gov.uk/policies/consumer-issues/consumer-white-paper

[8] Royal Society of Psychiatrists (2006) “Final demand” Booklet http://www.cfebuk.org.uk/pdfs/final_demand.pdf

[9] Money Advice Liaison Group (MALG) (2007) “Guidelines for money advisers and creditors to support the use of DMHEF” http://www.rcpsych.ac.uk/pdf/DMHEF%20GUIDERCPsych%20webApr%2009.pdf%20(2).pdf

[10] MALG (2009)  “Good Practice Awareness Guidelines For Consumers with Mental Health Problems and Debt” http://www.moneyadvicetrust.org/images/Mental_Health_Guidelines_2009.pdf

[11] Jenkins R, Fitch C, Hurlston M, Walker F (2009) “Recession, debt and mental health”  Family Medicine Mental Health  6:85-90

My #scipolicy News archive: November 2010

My #scipolicy News archive: November 2010

My #scipolicy News archive: October 2010 Part C

My #scipolicy News archive: October 2010 Part C

My #scipolicy News archive: October 2010 Part B

My #scipolicy News archive: October 2010 Part B

My #scipolicy News archive: October 2010 Part A

My #scipolicy News archive: October 2010 Part A

The sound of science :)

Science Policy News: September 2010 Part 3

I have to say that the last couple of weeks I have been a bit busier than usual so I have not been as attentive as I would have hoped with with the news. Saying this, there is quite a lot of papers in this archive so I hope that is still quite representative. :)

My #scipolicy News archive: September 2010 Part C

Science Policy News: September 2010 Part 2

So since no one complained, this is the new installment :)

My #scipolicy News archive: September 2010 Part B

i just like this image so i thought I should post it :)

taken from here

Science Policy News: September 2010 Part 1

I have mentioned time and time again that I am collecting news, and I am putting them into files. I thought of putting them online in case someone wants to read them. I thought maybe it will save some other people time. :)

PS because I am very careful with copyrights etc, all the articles say where I took them from. But if you find that this is going against rights of any authors, please tell me and I will not put them online. Thanks!

My #scipolicy News archive: September 2010 Part A

a small update - diary entry

You might have noticed I have been away for a while.

A side of me wants to say: "I wish I could tell you that I've been on holiday". This side is tired.

The other side, however, wants to say: "I have been working on a Youth in Action proposal for the EU!!!". That side is enthusiastic and full of energy.

Both sides are saying the truth. Writing a proposal from scratch by yourself is a difficult thing. Especially if you have no experience like me. I will tell you more about the event this proposal is about, if it gets accepted. I don't want to say anything else, in case I jinx it.

Now that the proposal has been submitted, I have finally started to look around me. 

Greece is nowhere near looking like this:

there is still time for:

but I have the feeling that children get around this time. Well... some children, i bet a lot of them don't. I always liked school because it meant I had a lot more company of my age - you guessed correctly I was an only child. So let me rephrase - I have the feeling I used to get as a child around this time: Athens is full of people again, shops are selling school things, the temperature dropped below the high 30s it has been for most of the summer, etc etc. All these lead me to think that a brand new year is starting. And I am highly optimistic and enthusiastic about it! :):)

This year will be interesting!!! For me and for this blog. I am continuing on my quest to understand the relationship between science and society, through my own reading. At the same time I am starting a Masters course on Public Policy and Management, so that i can understand a bit more the economics and the politics that affect Science Policy. If my proposal gets accepted I will have all sorts of other news. Maybe some news from my work too.

So I want to wish you a happy new year! :):)

Science and Society: My analysis of the Eurobarometer (1)

So I finally finished gathering my data and did my plots. Before I get into specifics about what exactly did the Greek sample say, I want to mention four things that I found striking:

1. there was significantly more emphasis in the Greek answers: Even though, in most questions their beliefs appear to be similar to those of other Europeans, their answers were more "emphatic" i.e. their answers were less divided compared to other EU countries. I noticed this by eye, and in an effort to "quantify" it, I ranked all European countries according to their responses using the graph charts presented in the Eurobarometer report. In these graphs, the countries were plotted in descending order, according to the value of the majority and minority percentages in those questions. The country on the far left was thus ranked "1" since it showed the greatest majority percentage. Similarly the country on the far right was ranked "28" (the average of all 27 EU countries was included in the ranking).
   
   In the following graph I present the distribution of rankings of the EU27 average:
   
   
   As expected the average of "EU27 average" (as calculated in the report) rankings was 15, i.e. in the middle. The EU27 average rankings ranged from 11 to 19.
   
   I did not calculate the rankings for all countries - that would be too much work I am afraid. I first calculated them for Greece and the UK, given that these are the countries I am comparing here. I also calculated them for Italy (as an example of another Mediterranean country), Germany (a central European country with a strong science base and a long history of science communication, to make sure that there is no "UK vs the continent" bias) and Denmark (as an example of a country widely known for being very technologically advanced and innovative).
   
   I could have chosen other countries for these comparisons. For example, I could have chosen Cyprus as the Mediterranean example, but a lot of the answers of the Cypriot sample were too similar to the Greek sample. I found this also very interesting (is this an example of how culture shapes people's relationship with S&T?).
   
   Here are the equivalent to the above plot for each of the countries mentioned above:
   
   When the graphs above are compared, one sees that the majority of the Greek sample's rankings tended to be a lot higher, whereas the  majority of the UK sample's rankings tended to be lower compared to the other countries. The average ranking for Greece was 9 and for UK was 17, whereas for Italy was 16, for Germany was 14 and Denmark was 14.
   The Italian, German and Danish ranking ranges look very similar - spread out over the whole range.
   
   
2. they replied a lot more than the EU average: the average "Don't Knows" for Greece was 2% whereas for the EU27 averages was 5%. Thus, Greek people seemed more sure about what to reply compared to all other Europeans. I calculated this to look at the "ignorance" factor, which could have lead to the above emphasis. I.e. it could be that the results in point 1 above were so striking because Greek people did not know what to answer. But this does not seem to be the case.
   
   
3. the Greek sample seemed a bit confused on what they feel about S&T: in many questions Greek people were positive about S&T but in even more questions they were negative about it. This is striking given the emphasis with which the answered these questions. More on this point in the following posts and in my concluding post.
   
   
4. the difference in the rankings of Greece and UK were striking: in most questions they were on the opposite ends of the plots!

So these are some general conclusions I drove from the whole analysis. In the following posts, I will look at those questions on which the answers were most interesting.

Research and more in crisis

On the 8th of July, my article on Research policy in Greece was published in ResearchEurope.

Why am I surprised?

One could say that in this blog, I focus too much on UK science policy news, or generally UK science-related events, trends etc. I have to admit, I find them a tiny bit easier to understand, given that I did all my studying in the UK.

But there is another reason why I focus on the UK. I am still a bit scared to look at what is happening in Greece. Probably, since 2002, when as a naive 2nd year undergraduate, right in the middle of my tree-hugging phase, I looked online to find out what my government's views were on GM. I was against GM back then, so I was happy to read that the Greek government was too. However, the reality was very different. Since the government did very little to control GM crops, there were many GM fields in Greece. If I remember correctly, they had to burn huge areas when they found out about them, in order to show they were truly against GM. I was very disappointed to say the least.

My problem with science policy issues - e.g. libel law, abortion, animal rights, MMR, homeopathy, etc - is that I have huge gaps in my knowledge since I only recently started to be interested in them. I have no idea what are the facts, what are the arguments for and against, for many of these issues. Immersed in my world of theoretical genomics, I did not really pay attention when I was in the UK. This was a good thing in a way, because I managed to get my PhD very young, but on the other hand, I now feel completely overwhelmed. Don't worry, you might say, there is plenty of time. You are right.

Homeopathy is one of the issues I know nothing about in terms of policy. I have met people of course that use it regularly, but i have no idea what is going on exactly with doctor certification, government expenditure, etc.

I have to admit that when I was 13 I went to a homeopathic practitioner. Well, I did not have an appointment as such: I was on holiday with my parents, when a common friend told me to go visit him at his holiday home. The reason she sent me was that when she gave me a massage, she found that apparently "I had too much garbage in me". I did not do the therapy he suggested for long - it was ridiculous! - and the whole story was forgotten. I still remember how traumatising the "garbage" thing was. But then again a lot of doctors have told me a lot of traumatising things, so that is a different story.

I only recently found out about the efforts of Dr Evan Harris and many many others, to make sure that there is proof that all homeopathic drugs provided by the NHS improve people's health better than a placebo. This is an idea that makes COMPLETE sense to me and I am finding it very hard to understand why would someone not agree with such a statement. Also, I only recently found out that homeopathic medicines are so diluted that the chances that you actually get what it says on the label are almost zero.

This is how far my knowledge stretches on the issue in the UK, and I have not had the time to find out what the situation is like in Greece.

Until yesterday.

It all started when my boss told me in the middle of a completely unrelated conversation "Don't you know about George Vithoulkas?". Of course I hadn't. "He got the Alternative Nobel Prize, look him up!", he continued. My boss is a bit like President Bartlett in the West Wing: he makes me look up completely unrelated things just for the shake of it (I have to say, I do not mind when he does this, given how poor my general knowledge is). So... I looked him up.

George Vithoulkas:

studied homeopathy in South Africa and received a diploma in homeopathy from the Indian Institute of Homeopathy in 1966. Upon receiving his diploma, he returned to Greece where he practiced and began teaching classical homeopathy to medical doctors at what eventually became the Center of Homeopathic Medicine in Athens. In 1972, Vithoulkas started a Greek homeopathic journal, Homeopathic Medicine. In 1976, he organized the first of an annual series of International Homeopathic Seminars. In 1994, he opened the International Academy of Classical Homeopathy on Alonissos, which provides post-graduate training for homeopaths

Vithoulkas has authored a number of books on homeopathy, two of which "Homeopathy: Medicine of the New Man" and "The Science of Homeopathy" have been translated extensively, and is currently writing Materia Medica Viva, a homeopathic materia medica or reference work on homeopathic remedies, to reach 16 volumes when finished.

All this won him in 1996 the Right Livelihood Award - known as the Alternative Nobel Prize - for his outstanding contribution to Classical Homeopathy.

Maybe he knows how outrageous it is that a postgraduate course for homeopaths exists officially at a Greek University, since he seems almost surprised when he boasts about it on his website:

But the climax of homeopathy’s educational recognition in Greece is the publication in the FEK (Government’s Gazette) (1912/issue b’, 29.12.2006) regarding the authorization for a Program of Master Degree Studies in the University of the Aegean for medical doctors and dentists with the title “Holistic Alternative Therapeutic Systems–Classical Homeopathy” (duration: 2 years- www.syros.aegean.gr/homeopathy). In this Program of Master Degree Studies will participate the International Academy of Classical Homeopathy and Professor George Vithoulkas.

What is the name of department that this course belongs to? The Department of "Product and Systems Design Engineering". This department which also provides one graduate studies program (5-year B.Eng. degree: Product and Systems Design Engineering) and another MSc studies program (Design of Interactive and Industrial Products and Systems).

In what parallel universe does a homeopathy course fit in a university that is mainly focused on engineering? How did the government give its consent for such a course??

My boss told me that it is the only postgraduate course in Europe on Homeopathy. I briefly looked it up and discovered that it is definitely not the only one: there is the Homeopathy by e-learning at School of Nursing & Caring Sciences, University of Central Lancashire.

Then I read at the website of the European Committee for Homeopathy

Postgraduate training courses in homeopathy for doctors are provided at universities in Bulgaria, France, Italy, Lithuania and Spain, in other countries at private teaching centres.
Homeopathy is an official part of the Continuous Education Programme for doctors in Hungary and Romania.
A lectureship specifically for homeopathy exists only in the Netherlands (Amsterdam), a professorial chair of CAM including homeopathy in Hungary (Pécs) and Switzerland (Bern).

And I quote only the part on postgraduate courses. There is more on where this came from.

So... On the positive side, Greece is not the only country that provides approved university MSc courses on homeopathy. On the negative side, one of the internationally most recognized supporters of Homeopathy is Greek.

Given that the positive side is not that positive and the negative side is very negative, this is of course a very disappointing reality.

But... why am I surprised?

Science and Society: step 2 is to plot the data...

This is just a teaser of the data i am plotting. This is maybe the question that has the biggest difference between Greece and the UK, but I am half way through all the eurobarometer tables.

So a lot more Greek people feel that "because of their knowledge, scientists have a power that makes them dangerous". When all EU27 countries are ranked according to their belief in this statement, Greece is on the one end of the spectrum (2nd most agreeing) and the UK is at the other end of the spectrum (6th least agreeing).

Could this maybe be part of the explanation to my question, for the difference between the two countries?

Science and Society: step 1 is to set the question...

Why is there reaction to science-related issues in some countries, and in others not so much?

Having lived for almost a decade in a country where there were big reactions to science issues (MMR, mad cow, etc), and having moved back to a country where the reactions are not so big - one could say non-existent - it makes me wonder why is this the case?

Of course it comes down to society, but why? What I mean is, of course there are big differences between the British and Greek societies, but which of these differences cause reaction in the former and not in the latter?

This question has been brewing in my mind for quite sometime now since it is different to communicate science to a society that is against it, than to a society that simply does not care. (A related question: why it does not care?)

Ι decided to set the task of answering the question above when I read the rapid response of some people in - once again - the UK.

In a recent comment, Guardian columnist Simon Jenkins (you can find the article here), basically said that scientists, with Martin Rees and Lord May as their archbishops, "just want money" "based on faith, not reason". Jennifer Rohn, two days later published a post in her blog were she "proposed making Monday," today that is, "Spoof Jenks day, with bloggers taking the opportunity to writing an anti-science post in the style of Simon Jenkins". The idea was well received and in just 2 days there were not 1, not 2, not 5 but 11 Spoof Jenkins posts (you can find them at the end of this post but for a more updated list please check at the original post by Jennifer Rohn). Please also use the "#SpoofJenks" hashtag on twitter.

So this is a science-related issue and there was a fast reaction from the scientists. (I am so damn impressed when the reaction is so great!). In other cases, it is the creationists that react fast. I does not matter who does. Here I am talking about the reaction itself.

It makes me wonder, why is it that in the UK, in France, in the US, in Germany, etc there are reactions whereas in other countries there are not that many? Is it just my unfamiliarity with Greek reality or is this truly the case?

So, for the next couple of months this is what I will be thinking about... any help, ideas, will be much appreciated!


PS. The SpoofJenks posts
1. Get over it, scientists: your cushy days are numbered
2. Urgent new priority for UK science
3. A Mammoth of Research
4.Jenks from tectum to rectum
5. Perpetual Poetry in Motion
6. Not a guest post and not by Simon Jenkins
7. Simon Jenkins collects his tithe
8. A day in the life of Simon Jenkins
9. We know too much
10. Cancer: Scaremongering 'Scientists' Ramp Up The Fear
11. Bloody scientists think they know everything

Skeptic Park: absolutely brilliant!

I haven't posted about things I found amazing for a while. The truth is I can't believe i just found this!

Can you believe there is a South Park for Science, Reason and Critical thinking?!? The blogger who made these amazing strips is Crispian Jago and his blogspot is: http://crispian-jago.blogspot.com/. Skeptic Park is absolutely brilliant as is of course his whole blog!!!!

EPISODE 1:

EPISODE 2:

EPISODE 3:

I can't wait for more!!!! 

an easy guide to remember what a SNP is

We read about SNPs (pronounced snips) in the papers and online, we hear about them on TV, on the radio and in people's conversations. But what are they?

A SNP is used to understand someone's Story - which population they belong to and who were his/her ancestors - and what makes them the Person they are - what do they carry in their DNA.

Thus, SNPs are used to find someone's S and P i.e. SNP.

----

A SNP stands for Single Nucleotide Polymorphism.

Consider our DNA as a very very very long road, with millions of houses - which we call nucleotides - each of which has an address - we call this its "position" or "co-ordinate". Thus when we talk about a single nucleotide, we talk about 1 of the, 6 billion in the case of humans, houses that make up our road.

There are 4 types of nucleotides/houses (we call these alleles): blue (Cytosine or C), green (Adenine or A), yellow (Guanine or G), red (Thymine or T). If the houses in the photo above were a nucleotide sequence, this would have been GCTATG.

But a SNP is not just a single nucleotide, it is a single nucleotide polymorphism. What is meant by polymorphism is that the house in the middle of the photo above, say the house with address 17854853, in my road is of a different colour than the house of the same address in your road. In this case, mine is green whereas yours could be blue. In biology talk, this is equivalent to "there is a SNP at position 17854853, where I have allele A and you have allele C".

In order for a house to be called a SNP, it is required for at least 1% of the human population to have a different type of house (allele) at that address than the rest. As a result SNPs are not very common: on average only 1 in 1000 houses is different between two individuals.

"So far so good" you could say, "but why is your house green and mine blue?".

The answer is mutation. When DNA gets copied (mitosis) or when it is split in two sets of chromosomes to produce the cells that can give rise to a new organism (the gametes, i.e. the sperm and the egg), mistakes happen. What I mean by mistake is that sometimes the house changes colour, but it can also mean that a house is destroyed (i.e. deleted) or a new house can be inserted.

But this does not exactly explain your question: it only tells you why our houses in this specific address are different, but not why my house in this particular address is green and not red, and yours is blue and not yellow.

This is where the S and P come in. My house is green and yours is blue either because our ancestors were different (the S part) or because a mistake was made when either one of us got created (the P part).

----

We' ll consider at the S part first. Lets say that the tree below is a tiny part of the "tree of life". I am the green dot and you are the blue dot. You will be happy to know that we closely related since we had a common ancestor just near the green line.

(image modified from http://dragonartz.files.wordpress.com/2008/12/_vector-tree-preview2-by-dragonart.png?w=495&h=495)

Our common ancestor had a green house at address 17854853 of his/her road. This ancestor had two kids, one of which is my ancestor and the other is your ancestor. A mistake was made when your ancestor was created and his house turned from green to blue. And just so that you do not get offended, mistakes are not necessarily bad. They can be good (advantageous mutation), bad (disadvantageous mutations) or they can make no difference whatsoever (neutral mutations). We now know that most often mistakes make no difference.

So the reason why my house is green and yours is blue is explained by who were our ancestors! Differences are explained by our history but this also means that looking at these differences we can understand our history. Find out what is our story. And this is one of the two reasons why SNPs are important: they allow us to understand where we come from and why we are the way we are!!!

Let me give you an example. I choose lactase persistence since it is a very clear and very famous example and because one of the people I worked with during my PhD worked on this.

Lactase is the enzyme that digests the lactose in milk. In some humans lactase activity decreases after weaning (we call these lactose intolerant). In others, lactase activity persists at a high level throughout adult life (we call these lactorse tolerant). Biologists wanted to find out how did this difference arise, what makes these individuals different. For this reason they had to find the SNPs associated with lactase persistence.

Two SNPs have been identified as the best able to explain why one individual is able to digest lactose and another one isn't. The first is "rs4988235 (−13910C→T)".

Don't be scared! All this means is that:

1. the name of the SNP/house is rs4988235,
2. the SNP/house is found 13910 houses before the start of the LCT gene, the gene makes the lactase enzyme (for the record the house's actual address is 136325115),
3. the house can be either of type blue (C) or red (T), and
4. the ancestral house was of type blue (C) so when one has that type of house is lactose intolerant, whereas if their house is red (T) they are lactose tolerant.

The other SNP is "rs182549 (−22018G→A)". You can now guess what this SNP is from my explanation above.

What Bersaglieri et al (2004) did was to look at those two SNP addresses in a number of individuals and count how many of them had one type of house or the other. In other words they wanted to determine the frequencies of the persistence-associated alleles (T in SNP rs4988235 and A in SNP rs182549). The individuals they used came from three populations (European Americans, African Americans, and East Asians) and for each of these individuals they knew if they were lactose tolerant or intolerant. What they found was a correlation between how common were the persistence-associated alleles and the level of lactose persistence in a population. European Americans, the population with the most lactose tolerant individuals, had the greatest percentage of persistence-associated alleles in these SNPs(77%). In contrast, the other two populations show low lactose tolerance and they have the lowest frequencies of persistence-associated alleles in these SNPs (13-14% in African Americans and 0% in East Asians).

So what did we understand about human history from looking at these SNPs? Based on this data, Bersaglieri et al (2004) estimated that these mistakes (C to T in SNP rs4988235 and G to A for SNP rs182549) rapidly became more common at a time near the estimated origin of dairy farming in northern Europe i.e. ∼9,000 years ago. They thus concluded that added nutrition from dairy appears to have provided an advantage in northern Europe. When dairy farming appeared, humans could not drink the milk. Mistakes happened in the DNA of some of these people and since being able to digest lactose gave an advantage, these mistakes spread through the population (i.e. the frequency of the persistence-associated alleles increased). In fact, these mistakes are in the top 3 of the most advantageous mistakes estimated to date.

------

Now lets talk about the P.

Our DNA does not only tell us about our past, but also about our present and our future. In other words, it tells us what we are and what does this mean in terms of our future. We get this information, in other words we understand what makes us the Person we are, when we compare our DNA to that of others. And one of the main reasons we want to do these comparisons is for our health. To predict what will happen to out state of health in the future. I will use cancer as an example.

Almost a decade after the sequencing of the human genome, new technologies have been developed that - given this sequence - make the creation of individual "SNP maps" or "SNP profiles" easier and easier. They also - and maybe more important - make it a lot cheaper.

But what are SNP maps? (I will use SNP maps from now on but SNP maps and SNP profiles are the same thing).

As I mentioned before, most of our DNA does not differ from person to person. Thus, in order to understand what causes our phenotypic differences - e.g. why do I get breast cancer and you are not - we do not need to compare the whole of our genomes. We only need to look at those addresses where there are known differences in the types of house found there. In other words we just need to look at the parts of our DNA which are polymorphic. Our SNPs that is.

A SNP map is like a registry that says what type of house (allele) we have in those addresses (houses) which are known to differ between individuals. It looks a bit like this: individual X at SNP rs4278313 (whose address is 105123) has allele C, at SNP rs9708285 (whose address is 105195) has allele T, at SNP rs9751025 (whose address is 105213) has allele A, etc etc.

But this is not the only source of information that doctors have for each cancer patient: they also know about their phenotype i.e. what cancer they have, for how long, what treatment worked for them and what did not, their sex, their age, their lifestyle choices, etc. etc.

You may now ask me "since doctors have all this other information, why are SNP maps helpful?".

The reason why SNP maps are important is that they can lead to faster and personalised medicine since they can be used

(a) for the better understanding of the cancer (red part of the following figure) but also

(b) for diagnosis and personalised treatment (blue part of the following figure) .

I would say that currently we are mainly using them for the former, but i will explain both of these below.

(taken from http://nci.nih.gov/images/Documents/f6e06278-e717-4465-b5b4-fda72f95584b/cancer41.jpg)

(a) understanding the biology of cancer: when scientists compare SNP maps of individuals with the same cancer, they can find in which SNPs these patients have the same allele and therefore which are the candidates for the cancer-causing mistakes (mutations). In other words, if individual A and individual B both have prostate cancer and they also have allele T at SNP rs4430796, allele G at SNP rs7501939 and allele C rs3760511 C, when men without prostate cancer have C, A and A respectively, then scientists assume that these SNPs are likely to be associated with this cancer. Of course these comparisons happen with a large number of individuals from many populations.

Similarly, SNP profiles can be compared to better understand the response to cancer treatments. If individual A and individual B both have prostate cancer, both got a lot better when prescribed a specific drug and both have the same alleles at a number of their SNPs, then scientists assume that these SNPs a likely to be associated not only with this cancer but also with this treatment.

(b) diagnosis and treatment planning: the stage above is aiming at personalised medicine. In the previous scenario it means that once the SNPs most associated with this cancer have been identified, a test is created to test each man for this set of SNPs. If they are found to have the cancer-causing alleles in these addresses then they have to check their prostate a lot more often than others who do not. In this way the cancer can be diagnosed in the earliest stage, increasing the chances of those people of living a long life. By the way, the first such test exists. A company called Proactive Genomics created two years ago the

Focus5™ Prostate Cancer Risk Test.

What stage (a) is aiming at is the following scenario: patient enters the room, doctor compares the patient's SNP map to the SNP maps of cancer patients. From this comparison the doctor is able to identify immediately, not only the specific nature of the cancer of the patient but also the best treatment for this particular patient. Cancer is diagnosed and treated at a very early stage and patient has less chances of dying because of the cancer.

However, we should not forget the ethics of this "mapping" and also to take into account the patient's psychology. Patients react differently to news about their health. They make a number of decisions some of which could prolong their lives, but others may have the opposite effect. The question you need to ask yourself is: Would you like to know that there is a probability that you will get cancer? Would you have liked to know this at the age of 18? Or 15? or 5? Would you like other people to know about this? Will it be possible for you to restrict who knows and who doesn't? How is this knowledge going to affect your life?

-----

So from now on, when you see or hear something about SNPs remember your S and your P: remember that the importance of SNPs is that they can tell us things about our hiStory and they can lead to Personalised medicine.