Friday, 10 October 2014

Data Driven Biology

This is where biology is going to go. Everyone always thinks that biology is the easiest of the sciences, but in terms of building models and making predictions it is by far the hardest. Maths and physics are trivial by comparison to modelling even the simplest living creature.

We need more data, more computer power and more maths to generate theoretical biology. It has been tried many times before, the last version was systems biology that fell flat on its face with excessive claims and little foundation. So what next?

Biology with:

  • Remote sensing.
  • Continuous monitoring.
  • Multiple level measures (from the molecular to the whole organism).
  • Microfluidics.
  • Next Generation Sequencing.
  • Medical Informatics.

Saturday, 4 October 2014

Bill Maher is wrong it is Islamophobia





I wrote this in response to this video posted on Facebook by Bill Maher. I usually like Bill but over Islam he is wrong.

Lets have a look at what Christianity looked like after 1000 years of its creation - they were cutting breasts off women who believed in free love, burning women and non-Christians. The muslims in Spain tolerated other religions until they were massacred by the Christians. Jihadists are no different to the crusaders. There was no equality and there were no Liberal views.

Those are inventions of the last 100 years at the most. Even 100 years ago the "Liberal" Christian west was no better. Until the 1960s homosexuality was illegal in the UK. Until the 1920s women could not vote even in the UK.

I am a Liberal. IS is an abomination but conflating it with Islam is stupidity and Islamophobia. Sam Harris throws his statistics about British Muslims but who carried it out? When and where? You win by changing minds and educating not by painting everyone as an enemy. On this I think Bill is wrong and that he has been misled by his views from the skewed US media. He can say the Koran says xxx to homosexuals and apostates and women, but so does the Bible. No Jewish or Christian follows the bible literally so why does he think muslims are going to be literal about the Koran? They are more Conservative with regard to religion, but so is the entire US compared to Europe.

Here are some muslim attitudes statistics for Sam Harris to think about

http://ukpollingreport.co.uk/blog/archives/291

Or he could look at the schlock polls which are biased and non-systematic which do show increased Conservatism in second generation migrants - much the same as found in the US.

http://my.telegraph.co.uk/danielpycock/danpycock/956/what-do-british-muslims-think-of-the-uk/

Wednesday, 1 October 2014

Standing out

This was part of a spam e-mail I got about Optimising HE Curriculum Design
Last year, Sir Michael Barber, the Chief Education Advisor to the world's biggest education firm, Pearson, claimed that Universities must, "mark themselves out of the crowd or risk an avalanche of change sweeping them away."
This actually is a statement about the problem and not the solution. Pearson, McGraw-Hill, Palgrave-Macmillan and the others are all trying to get as much as they can of the multi-billion pound education business. What they want to sell all are complete educational packages of textbooks and content that will all be assessed using their examination boards. Then you will go on to Higher Education and study for a Pearson or McGraw-Hill degree from the University of X or Y as accredited by the publisher. We will end up with cloned students who become cloned graduates. It will be a statisticians dream. All of those norm measured exams, all those nice symmetrical distributions. Governments will love it especially education ministers talking about standards and fairness and how everyone gets the same opportunity. But it will be terrible. It will be an abomination.

Why would we want to train these robots? That is not an education. What can the world do with all of these homogeneous graduates who excel at doing exams and cannot tie their own shoelaces? Where are the real skills? Where is the questioning, the rebellion, the life of a student just finding things out? The world would be a much poorer place if we let them do this. So Sir Michael is right, there is a warning that we need to be progressive and to stand out. But that means standing against the academic publishing behemoths to create an education that is built for purpose and not for profit.

Tuesday, 16 September 2014

Some teaching reflections

I suppose I like to be awkward and perhaps yesterday I was more confrontational than is useful but some people need to know some truths and to start thinking and not being comfortable. The powers that be in the place where I work have decided that we need to redesign all of our courses and module moving to 20 credits from 15 credits. This is also an opportunity to improve our teaching.

Where I start from

I am a progressive. I hate lectures as they are poor learning/teaching events. I want students to be good thinkers and creative. I hate restrictive marking criteria and inflexibility as it does not allow you to properly assess students and for a statistician I think that quantitative methods in education are over-rated and over used as these are artificial and actually destructive metrics. The actual measures of success if the futures that your students have. So for me the League tables with the national student survey is a pointless distraction. The doctor gives me cough mixture, if they ask me if I like taking it I will say no, but it doesn't mean I don't get better and like its effects. The same with students. You ask them about courses when they are taking the medicine not when they have a job and they have recovered.

I talked about an experience of teaching a flipped classroom to 100 students and said how well they had done. So I was asked if the students liked it. 10% hated it and so there were all the grumbles about the student questionnaire. When I said I do not care about the 10% hating it there were even more grumbles. But let me reflect on that does the student questionnaire doesn't say do you hate bioinformatics? It says do you hate the university teaching and they hate the boring lecture far more. I meet my KPIs and student performance is good. They if they reflect on it find that they enjoyed it more and got more out of it. The ones who didn't are the non-reflective students who want to be taught but not to learn. We are not educating if we dumb down to that level, and we are not making the most of our students. But this illustrates the current fear of student feedback, which will become worse as students become "customers".

Teaching Anatomy and Physiology

Talking to the students these are courses that they hate. They are facts, facts and more facts and memorisation. I am a chemist by training and at my university they wanted us to learn the periodic table. The question is why? What good does it do students? Knowing what it means, as in which are metals, which are most reactive which is functional knowledge matters but the actual names of elements in their right places is irrelevant when I can look it up. 

Almost all groups agreed to condense the course and make it less broad but deeper and more about getting students to understand the complex concepts. Except the traditionalists who are worried about professional accreditation and want the students to know all those facts. So I asked why and they say about people putting the liver on the wrong side of the body. Ok so why is that going to cause a problem? If you are a doctor and diagnosing it might but they aren't going to be doctors they are going to be bio-medics and work in diagnostic labs where the need to know where the liver is will not be a daily question, and if they do want to know they can look at an anatomy chart. 

Isn't anatomy implicit in the physiology? Everyone else teaches it this way rather than wasting 20 credits on the tedium of anatomy. No there are important details they say. So what is the difference between endothelial and epithelial cells. As a non-biologist I replied that one is inside and the other is outside which is their literal meaning. But no this is not good enough they need to know more for anatomy. Why? I cannot quite work out why you need to know anything about their anatomy when the main differences are to do with proteins used in their connective structure and that endothelial cells do not promote thrombosis. So that is the lesson the physiology of blood flow their anatomy is IRRELEVANT. When you do need it you can look up a picture of their structure and an article on their composition. The functional learning is about clotting.

The final argument for doing it the old way was that recruiting was solid. That is a fools argument. It might be now but if you can't make yourself distinctive and show why you are better than the same tedious rote learning in other institutions higher in the league tables, you are soon going to be out of a job. As the Red Queen tells us you keep running to stay still. 

Facts, facts, facts

I am strongly against fact based courses. My colleagues argue that you need to know some facts to be able to construct more complex models and this is true but often not the ones we identify as important and not at the level we think they need to know. 

One of my colleagues gave an example of adding 2+2 as a fact. They did this because I am the maths person here and it is not a great example but it actually illustrates my point quite well. In maths addition is a functional knowledge. I do not store as facts all of the possible numbers I could add together in my mind. I memorise the odd ones but then I know the functional knowledge of addition. The same is true of multiplication. People who do mental maths each have their own special ways of cutting up calculations mentally. Trying to teach these to others with these mental maths skills is a bit of a pointless exercise as everyone has a different way of doing it. But most of the time pattern recognition helps and functional rules like odd numbers and even numbers and multiples of 3 divide by 3 - a very smart person can see why this is true in a decimal system.

So maybe we need to know that the liver does a lot of catabolic functions and what catabolism is, or that the kidney does filtering and homeostasis functions but do we need to know the air-speed velocity of the unladen swallow?

Monday, 25 August 2014

Casual Misogyny in the Evening Standard

I was reading David Sexton's film review for Lucy. It starts by calling Luc Besson the action-frog. Hardly an inspiring start to a review. But it was his description of Scarlett Johansson's lead character Lucy that was even more shocking.

"... she plays a dopey, gullible American student in Taipei, tricked by her boyfriend of just a week into becoming a drugs mule 'for ruthless Korean gangsters'. ... But when one of the thugs gives her a kicking, the bag bursts inside her and instantly makes her amazingly intelligent, fast and deadly..."
"Lucy, who up to this point has not been the sharpest knife in the drawer, wakes up superbright, impervious to pain and a lot more focussed, ..."

Nothing too objectional yet, except there is a tangential association with being dumb and being a female student, but surely if you are a student you have passed exams and might not be quite so stupid, naive perhaps. There is also the implication that she is easy with her boyfriend of one week. Every partner is of one week sometime, then it becomes two weeks etc. Then comes the last three sentences of the review.

"She becomes a sort of supreme internet, a popular conceit for obvious reasons, but not my idea of a dreamy outcome for the belle of the ball. Personally, I preferred Scarlett as she was on 20 per cent brain power. Or even a slutty 10."

Stop there, so he is saying a normal woman using 10% of her brain is slutty? Is he implying she is slutty because of the 1 week boyfriend? Or because she is blonde and female? Whatever way this is casual, everyday sexism. You might think that she was more fun to be with when she had the normal brain power than the souped up genius, but why does this mean she is a slut? If you can throw the word slut around so casually what does it mean about you opinion of women? It is this sort of misogynistic comment that feminist campaigners still have to fight. It is embedded in a lot of society and male culture, although there are some modest improvements. But for me this was unacceptable and I prefer to read Larushka Ivan-Zadeh in the Standard's sister paper the Metro, even with Daniel Craig's urgent penis .

Thursday, 15 May 2014

Quackery of Investment


This is what everyone is actually doing. You are just seeing if your system/model is better than the oppositions. It is like a poker game where the key is finding the other person's system. Once you get ahead (Goldman-Sachs) then you always win because you can always raise the stakes until the game is too rich for the opposition (Lehman Brothers).

Thursday, 8 May 2014

Player Piano

I have just finished reading Player Piano. It has some very memorable speeches and some very brilliant observations about people, but it is part of a cycle. We face the same dilemmas now. Do we want an automatic world? Would we be happy living a life of leisure while the machines do everything?

This machine Utopia has been coming ever since we invented machines, and it has been strong since the beginnings of the industrial revolution. The push-back is just as old. Vonnegut is telling the story of the Luddites campaigning against the automated looms and spinning frames. This was fictionalised by Samuel Butler in his novel Erewhon. Now the push is towards letting computers run our lives. This has been the inspiration for a lot of science-fiction authors. My favourite is Frank Herbert who wrote about this conflict in his Dune series. There the humans rebel in the Butlerian Jihad (a nod to Butler) and the machines of Ix are replaced by human computers enhanced by drugs - the mentats. But you do not need to look to science-fiction to see the rise of the machines.

Today I stood at the station listening to the automated message telling me that the next Circle Line train would leave in two minutes as I watched it leave as I go too late to the platform. Then the electronic screen told me I had 9 minutes to wait for the next train, before 3 minutes later the next automated message told me that the next train had just left Royal Oak and would be there in 2 minutes. As the echo of the message died away the next train arrived. Two minutes is shorted than I remember. At least I got to work a little earlier than I had anticipated. There I found a parcel from an online book-seller (not that one) that had been despatched by machine from a warehouse labelled and managed electronically. I was surprised by the contents as I couldn't remember ordering a teen fiction novel about a dancer. So I checked my order and it was supposed to be a textbook on epidemiology. So this is what we get with our technological, quality assured lives. The machines aren't going to take over the world anytime soon.