Definitely not.

At The Institute this year, I've got this rather sharp class of second year sporty-people.  It's good fun because they are able to motor on ahead, they seem to be getting something from the class and they help each other out.  I've been able to find some interesting data to analyse and they come up with interesting ways for processing the information.  The class runs in parallel with a series of more formal lectures on the theory and practicality of statistics, so we were requested and required to sort out the definitions of some statistical terms. This can be a rubbish assignment as it's easy to slip off to wikipedia and copy down the first sentence of the appropriate entry or, because that's plagiarism <shock horror> you try to  paraphrase that first sentence while engaging as little of your brain as will accomplish this task.  Five minutes, let alone five days, later you've forgotten 90% of what you have 'learned'.

A slightly different approach occurred to me when I was driving to work on the morning. a) Ask everyone to choose 3 or 4 out of the dozen or so head-words rather that slugging through the whole list. b) Put the submitted definitions in a long list and ask the rest of the class to decide which of the head-words is being defined. c) Offer a prize to the person who submits the most transparent definition. That worked rather well although it was a bit of work for me to fillet out and discard the head-word from each definition make the font uniform and print out the list of head-words [see immed below] and the list of defns.

1.Test of hypothesis	4.Statistical test	7.Significance level	10.Normal distribution
2.Control group	5.Blind experiment	8.Placebo effect	11.Degree of freedom
3.Test group	6.Double Blind experiment	9.Student’s t-distribution

First task is for you, dear reader, to have a punt at defining any of these in words that your mother (a redoubtable and intelligent woman with no training in science) could understand. The next is to see if you can work out what is being defined in the following list. In the original exercise, the terminal check box was empty and the students had to enter a number between 1-11 to indicate the concept be defined. The numbers entered here are the number, out of 10, of fellow-students who grasped what was being defined.

1. a statistical test that is used to determine whether probability that a given hypothesis is true  [8]
2. A group isolated from the experiment so that they provide baseline to compare the results of the experiment against [10] >!Prize!<
3. some kind of “fake” treatment, where no effect on the health of the patient it is administered to can be attributed to the treatment itself  [8]
4. Commonly, two statistical data sets are compared, or a data set obtained by sampling is compared against a synthetic data set from an idealized model [3]
5. where neither the tester nor the volunteer knows the outcome of the test until it has been completed  [9]
6. Suppose the test statistic is equal to S.The P-value is the probability of observing a test statistic as extreme as S, assuming the null hypothesis is true.If the P-value is less than the significance level, we reject the null hypothesis.The region of acceptance is a range of values.[2]
7. receives no additional treatment or neutral treatment [8]
8. A group of subjects who are exposed to the variable under study: a lower infection rate in the experimental group that received the vaccine.experimental group in Medicine Expand [8]
9. Receives additional treatment in order to view any occurrences which may appear during specific testing [6]
10. A procedure which contains inputs known as samples and the results obtained are known as a hypothesis.It includes a region of acceptance.It offers a mechanism for making measurable decisions about certain processes.[4]

In my post-mortem on the results, I pointed out that the scores for effective definition ranged from 2 to 10.  The Pink definition is full of scienciness but foxed pretty much everyone so that's not a very good definition.  I then continued "The chap who did number two, however, wins the prize for clearly expressing himself" there followed a dreadful pause as I realised what I'd just said before the whole class dissolved in general "teacher said potty" hilarity. The prize being a bag of Werther's Original, in honour of my pal Karsten who was born in the company's home-town: it was big enough to share.

Note for non-English speakers or people under the 

age of 30: "doing number 2" is a Victorian nursery
euphemism for having a bowel movement.

Global Handwashing Day

That would be today.  I have my first Food and Fermentation Microbiology class this afternoon and I'll be wearing a badge with the official logo [L] on it on my sleeve to indicate that I am showing solidarity with The South where a million children die each year from infectious diarrhoea. The other big killers covered recently on The Blob are TB and malaria.The Handwashing experts reckon that running-death can be reduced my 25-50% if enough soap is distributed and used effectively at key times of the day.
If you work with students or youngsters you might mention the day that's in it: raising awareness of the troubles of the Third World can do no harm

Who dreams these Days up?  In this case it's not WHO, although it could be. In fact it is the Global Public-Private Partnership for Handwashing with Soap (PPPHW).  The fact that the sponsors include Unilever, Colgate-Palmolive and Proctor & Gamble shouldn't get in the way of the message.  It is also endorsed by UNICEF, USAID, the World Bank and the London School of Hygiene and Tropical Medicine. When I saw the wikipedia entry in the cold light of pre-dawn this morning

I misread it as:
as 1.1 ...
1.2 Arms
and thought that tomorrow might be designated All Over Wash Day.  But I'd be wrong, it is, for historical rather the PPP reasons, rather World Anaesthesia Day.  Every day is a Day!

Endorse-bombing

There are a few of us who haven't signed up for Friendface. I don't have enough friends to make it worthwhile and I'm not really interested in seeing pictures of their children and grandchildren.  Once you've seen one child gurning gapped-tooth at the camera, you don't have to see more. These social-media sites come and go. Bebo died when the number of single men masquerading as teenage girls outnumbered the actual girls.  Some professional social-media sights seem to be gaining traction. I think I signed up with LinkedIn shortly after that enterprise started but as a very early adopter there was nobody there to smooze with, so I've long since forgotten my login details. Now that 5% of everybody is an active Linkedee, it's too crowded to give users any Masonic-insider advantage.

ResearchGate was started in Germany in 2008 and is meant to be for scientists only.  Nevertheless there are 7 million users including, since the end of September, me. For several months, I'd been getting e-mails from ResearchGate telling me that colleagues and co-authors were really anxious for me to sign up so we could all collaborate more vigorously and share data more equally. Aftre ignoring this spam for a long time, I was talking about it with my MSc student and . . . caved.  It was a bit of a bore. I had to do a lot of work for RG to help it/them establish just how broad and extensive my research career has been.  With many previous sign-ups associated with me, RG had a good idea of which papers were mine but before I could change my photo into something rugged, I had to trawl through a long list of publications by Scientist Bob, Scientist BT, Scientist B, Scientist TB, Scientiste B as increasingly unlikely guesses by the RG robots. Each one of which I had to claim or deny.  The default/suggested photo was kind of weird because it was clear that RG had looked for Bob T Scientist on images.google.com and come up with a cartoon of cats from my peripheral involvement with the Irish Times crowd-sourcing cat genetics project from earlier this year. The whole registration process was not without value because I was able to claim as publications a handful of book-reviews I wrote in the later 1990s.  Everyone knows that these are not 'real' pubs because they are not peer-reviewed but they were are worth reading nevertheless.  on 3rd October I received an email with this banner:

. . . a very low bar has been negotiated, so tentative huzzah.

I've been getting 3-4 e-mails daily from RG ever since, trying to stir up my interest in other RG people's doings:

• a chap who wrote a paper with someone I wrote a paper with [I danced with a man who danced with a girl who danced with the Prince of Wales] has written another paper about egg-yolk.
•  a chap from India has viewed my profile
• please 'endorse' the expertise of my Head of School at The Institute

This last is kind of weird because you're really doing RG's work for them. If my HoSch is claiming expertise in motorcycle maintenance, am I expected to scotch the lie?  A couple of days ago I got a message that my pal El Asturiano had "endorsed my expertise".  So I looked to see and discovered that I was meant to be an expert in 'cats' and assumed that El As was making a game of me.  Accordingly, I went to his profile and added "Asturianism" to his list of talents. The next day he added something peculiar to mine:

I guess my ability to make mince-pies at Christmas (and I've won prizes for that) is more useful and interesting than everything I know about biofertilizers which is just horse-manure.  I thought my coinage was a) damned clever b) original but it's been around for a while, having a tumblr site and[slow-load warning!] buzzfeed traffic.

Ada Lovelace Day 2015

Dang! Almost missed the day to celebrate Women in Science in UK and The World.  Someone is bloggin' about it. And the official site is up (as it has been for a couple of years).  There aren't many events really, even Worldwide. But there have been a number of STEM-women stories put up on the website as links to blogs.  I contributed a few in 2013 and added my trib to Mary Mulvihill this year.  Could someone remind me, with notice, next year and I'll get ahead of the posse.

ungaslight

Gaslight is a creepy George Cukor film from 1944 starring Charles Boyer and Ingrid Bergmann here's the trailer.  You can see the whole of an earlier less hystrionic 1940 British Thorold Dickinson production starring Anton Walbrook and Diana Wynyard. The word has been subsumed into the English language along with hoover, xerox, kleenex and thermos: much to the annoyance of the corporations who want to trade on their invention. Gaslighting is a process whereby one tries to convince another person that they are losing their memory, perception or wits; rarely now by causing the gaslight to dim in a rickety Victorian house. You might think this is a rare enough occurrence but I did come across a thread on Quora the other day which gives numerous examples and a romp through the language of personality disorders. It can be extremely wearing to be party to such a transaction - either as gaslighter or gaslightee - so compassion is a better response than anger. We live in a very negative world: Google reports 10,000x more gaslighting hits than its antidote.

I had a nice case of the opposite, which I will now call ungaslighting, at The Institute last week. Two hours a week I have timetabled for QM Quantitative Methods with our 1st Year scientists, but we might also call it RM remedial maths. It's what we must do to combat the math-deficit among our incoming students. The bulk of the course in the first term is practice-makes-perfect on key math issues and we have used KhanAcademy for this purpose in the past but recently have switched to www.mathtutor.ac.uk a handy pro bono publico project launched by Loughborough Polytechnic University in East England. Mathtutor provides a PDF tutorial, an explanatory video and some exercises for each topic. Last week it was logarithms, the finer details of which are a bit head-wrecking, so you may need to read my earlier pitch for logs. On the front page of the mathtutor PDF are the Rules of Logs:

• log(ab) = log(a) + log(b)
• log(a/b)=log(a) - log(b)
• log(a^m) = m log(a)

With that, even if you don't know exactly what is a logarithm, you should be able to answer a question like: determine the value of N, giving the answer as a whole number or a fraction.

In my Friday class is a very shy, very young-looking feller who is quite good at maths based on the result of my prequiz.  I have him marked down as "no probby", but halfway through the session he had his hand up asking for help on the question above. His answer was 2592/64:

N = 2⁵ * 3⁴ / 4³ = 32 x 81 /64 = 2592/64

but The Computer [must be right is wrong!] was holding out for 2025/64 so he thought that he was missing something important. He looks like the sort of chap who has been told that he was wrong rather a lot: wrong haircut, wrong shoes, no piercings, no girl-friend etc. so has had a lot more tentativeness than assertiveness training.  But I assured him that he was correct and the computer was wrong . . . or at least I agreed with him and not the lads in distant Loughborough.  But I also said it might help if we find out why Mathtutor thought 2025/64 was correct. Find out why is, after all, what science is all about. Knowing your 81x tables helps: 25 * 81 = 2025. So Mathtutor had given the wrong, wrong almost right answer to log(N) = 2log5 + 4log3 - 3log4.  This is not the first typo we've discovered in Mathtutor and typos are a far more valuable learning experience than motoring through pages of exercises. If I was Loughborough, I would pepper in a few deliberate errors to jolt punters out of glazed-eyed sleeping-walking through the exercises. And my young chap can go home saying that he beat the Internet, which can't harm his self-esteem.

Bleeders

One of the miracles of physiological function is that we don't exsanguinate ourselves when we have a finger-mishap while chopping onions. We cry "Oh Bugger", stick the digit in our mouths, hop about a bit and almost before we've got a sticking plaster ready, the bleeding has stopped. Evolution has encountered similar damage before and caused the development of a series of biochemical events that tangle up the disappearing red blood cells in a web of protein and cell fragments called platelets to staunch the flow. It works but b'god it's not as simple as slapping on a plaster and uttering an imprecation. Like yer foot bone's connected to yer ankle-bone etc.etc., the damage is detected and then requires a cascade of at least a dozen molecular events, each controlled by a protein. There are so many of them that science gave up giving them informative names and just numbers them: Factor I to Factor XII.

Damage -> FXII -> FXI -> FIX -> FVIII -> FX -> FII -> FI -> CLOT!

We only have 23,000 protein coding genes to do everything, so it's interest that 1/1000 of them do this simple but vital task.  Actually, you should reflect that the wall of a small blood vessel is only one cell thick and it is micro-repairs at this level that are the day-job of clotting factors rather than dramatic accidents with hatchets and saws. A bruise for most of us is the slowly discolouring evidence that a sub-cutaneous bleed has been repaired. Hemophiliacs dream wistfully about getting a bruise, because they don't - they just bleed and bleed and it hurts. Hemophiliacs are those who are missing one or other of the Factors so they don't clot so good.

Last 27 November 2014 Nature put out an excellent multi-page supplement on Haemophilia and it's therapies which in contrast to the one on Liver Cancer, which I filleted last month, is not pay-walled.

It's not red or white; all or nothing. One hemophiliac may have a totally banjaxed Factor VIII, while another replaces glycine with valine at position 89 and can have something approaching a normal life.  Indeed your FVIII protein may be different from mine but both are sufficiently active for both of us to be in the normal range. The key theme in my Human Physiology course at The Institute is the idea of homeostasis and how amazingly good we are at it. Too sensitive a clotting cascade and we'll be getting deep-vein thrombosis every time we sit down to an episode of Neighbors rather than waiting for a long-haul flight.

There are +7 billion people on the planet today, of which about 180,000-350,000 have some form of hemophilia. To put that in some sort of utilitarian perspective 180 million people are infected with hepatitis C virus.  When the British Queen Victoria's fourth son was born with hemophilia in 1853, they could afford to keep him safe from slings and arrows and accidents but there was no effective medical intervention and he died (a trivial slip and fall led to a brain hemorrhage) at the age of 30. By the middle of the last century, hematologists knew enough about the process of clotting that they were able to concentrate the Factors by freezing whole blood and making injectible quantities available for therapeutic use.

That was better than nothing but the therapy was not without its problems. While the rest of us have a neat and delicate feedback loop to maintain the levels of Factor VIII and IX at a Baby-Bear just-right level, hemophiliacs were getting a gurt big lump of the stuff all at once. Normal Factors, along with pretty much all the biochemical bits and bobs in the circulation, have a turn-over time or a half life: old product is broken down and recycled and fresh stuff is made continuously. So Problem #1 for added Factor is that it doesn't last. Factor VIII is half gone in 8-12 hours, Factor IX lasts about 2x longer.  There is a lot of work going on in Big Pharma to extend these biological limits, so that the poor kids need to prick themselves less often. But it's been slow progress: the current best hope is Novo Nordisk's N9-GP which has a half life of 110 hours or 5x baseline. The longer time extensions all apply to Factor IX which is 1/6th the size of Factor VIII.  That's a bummer because 80% of clinical hemophilia is due to Factor VIII mutations.

As if getting a duff hand of cards from the genetic lottery wasn't bad enough, cock-ups in the blood transfusion industry allowed donors who were HIV positive to infect pretty much all the hemophiliacs who had access to Factor replacement therapy through the 1970s. They need so many 'units' of Factor VIII and so often that it was hard to avoid getting a contaminated batch. In the 1980s, after they'd started to screen for HIV, lots of hemophiliacs were infected with HCV because The Transfusion-Man failed to screen for that. Thanks a lot lads!  By 1989, molecular biologists had developed a genetically engineered form of F.VIII and in 1997 a GM F.IX was available. No chance of further viral contamination there. My tree-hugging anti-GM pals might reflect on that while they chant "Monsanto Bad Wakantanka Good" and dig up GM turnips in the remoter parts of agricultural research stations.

Another problem is the immune system. This teeters very day on a tightrope trying to recognise foreign proteins as potential, even probable, pathogens.  Believe me, it's wild world out there full of hostiles big and small - nematodes, bacteria, fungi and viruses - and you'd prefer that the immune system 'neutralises' pretty much anything it hasn't encountered before  . . . unless it's therapeutic Factor VIII.  But that much nuanced discrimination is often a bridge too far for a system working full time under unforgiving circumstances. This natural response is called factor inhibition and BigPharma is working in another part of the factory to develop anti-anti-bodies to neutralise or at least slow down the immune system to let artificial Factor VIII and IX carry out its essential task.

Finally we might ask why BigPharma is interested in hemophiliac treatment. It's not only about the money but a lot of it is sloshing about earmarked by medical insurers both private and socialist for treatment of hemophilia. In rough terms, a unit of Factor VIII costs $1.  For prophylactic dosage, an adult needs about 25 units per kilo body-weight or $1750 a go. 2x or 3x a week every week for 52 weeks a year that's the bones of $300,000 a year. If half the hemophiliacs have access to replacement therapy we're looking a retail price of $25 billion every year globally. In Ireland there are about 200 hemophiliacs, whose (€60m/yr) bills are picked up by the Health Service Executive. Only the hardest Utilitarian is going to ask what else could be achieved with that much money.

Updates 11 October

Surfing the standing wave [Vimeo 3:30 mins]  No more bobbing about in the sea waiting for the wave and you don't need to shell out folding money to surf.  Now you just need a wet-suit including neoprene gloves (because its cold out there ["groundhog"]) and surfboard and a river in spate conveniently close to a highway. While you're out off your sofa and allll wet you might go down Puerto Rico way for an arty Surfers vs Technologia film [Vimeo 6.25 mins] those dudes are carving some gnarly tubes.

Remember Primo Levi? And his brilliant book of sciency stories The Periodic Table? Well his Complete Works is out for a hefty price £56 / $63 until you reflect that it is >!3000!< pages in three volumes with a slip-case.  Clearly the Christmas present for those who spell Oświęcim with the correct accents. The review / retrospective in the New Yorker is also worth reading. It reflects sensibly and sensitively on his accidental/suicidal end. While you're about it, read a short story Quaestio de Centauris by the great man?

Remember Hans Rosling talking about life expectancy and coffee-cups?  This tells you to turn up on our mountainside for my burial shortly after 23rd July 2038. Obviously your mileage may vary but you're unlikely to do longer than me with a Granny who hung on till she was 108 and a Gt-granny on the other side who died at 103. And on the subject of death, I don't think I've posted about Years of Life Lost, YOLLs [3.15 min vox video] a sort of counter-QALY.

Alison Gopnik? What about a predictably radical critique of school-based education which Gonnik finds to be neither sufficiently persistent about practice-makes-perfect learning nor at all interested in real enquiry-based learning.

Remember the Royal Society and their recent desire to make videos about its connexions more widely available? I've just heard about a RS channel called Objectivity in which Numberphile filmista Brady Haran gets access to the Royal Society Library card catalogue. It's a channel so you'll have enough to keep you going while sporty people are watching Ireland and France play rugby this-arvo. What about hefting the standard yard and the standard pound? Super historic cool.

While I have your attention, I'll mention that, since 1988, 11 October has been designated National Coming Out Day. I guess that makes it LGBTQNCOD. Which is a bit of a mouthful. The Irish Examiner decided to interview Katherine Zappone and Ann Louise Gilligan whose Canadian marriage was unrecognised by the Irish Supreme Court in 2006. And HuffPo has some more nuanced advice on the pro & con of out.