Ten papers for ten years

Scientific paper clip-art

Scientific paper clip-art

Blogging Beyond is about ten years old now

To celebrate, here are ten papers I like, in chronological order by publication date. Each is accompanied by a short justification for its inclusion in this list. 

  1. Ridge Regression: Biased estimation for nonorthogonal problems (1970) Technometrics Hoerl and Kennard [pdf]

    This paper sets out the statistical technique of ridge regression. This method formed the basis of much of my PhD thesis. I read this paper so many times, and had so many highlighted and wrinkled printouts kicking around, that by the end of my studies I could almost recite it. I learned matrix algebra and the canonical form of the linear model from this paper and related ones. After spending so much time singular value decomposed, when it comes to linear modelling, I think in projections. I find the sums of squares mentality much harder to get my head around. (Those last sentences are for the stats people.)

  2. On being sane in insane places (1973) Rosenham Science [pdf]

    Often referred to simply as the Rosenham experiment, this study of what madness is and is not, is not of itself particularly strong scientifically – I am always a little puzzled as to how it ended up published in Science. Nonetheless I like the literary style, amusing story, and the message about madness and what it means and does not mean in different contexts. A personal choice, perhaps somewhat revealing.

  3. Simple mathematical models with very complicated dynamics (1976) May Nature [pdf]

    This elegant self-styled interpretive review discusses the complicated dynamics that can arise in systems described by first-order differential equations. This paper was my entry point into dynamical systems, an area in which I no longer work. I did publish on the topic, albeit tangentially. I do not have many regrets about my academic career but I do regret never submitting the work that comprised my undergraduate thesis for publication. That work related to this topic. At the time I thought the work unworthy of publication. These days I look back and think what a pity that was. Imposter syndrome is a real thing. To be clear, though, my work was not a patch on May’s paper.

  4. Can a Biologist Fix a Radio? — or, What I Learned while Studying Apoptosis (2002) Lazebnik Cancer Cell [pdf

    I recommend this essay regularly to colleagues who are struggling with the interface of biology and mathematics. Not many people to whom I have recommended it, read it. I like it though. It makes me laugh out loud. 

  5. Subnets of scale-free networks are not scale-free: Sampling properties of networks (2004) Stumpf, Wiuf and May PNAS [pdf]

    I think I mostly liked this paper because I (thought I) understood it and that made me feel clever. I’ve not read it in years. The May on the author list is the same one who wrote Simple mathematical models with very complicated dynamics.

  6. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (2007) The Wellcome Trust Case Control Consortium Nature [pdf]

    This ground-breaking paper presented a collection of interconnect GWAS with a large sample size for the time. This is the paper I presented as part of my interview for a place on the PhD program at Imperial which I later completed. A fun story: candidates were given a free choice of papers to present, and asked to bring multiple printed copies of their chosen paper (seven copies, if memory serves) to give to the interview panel. This paper is long and I spent all my printing credit printing it out multiple times and carefully stapling. None of the interview panel wanted a copy, gesturing that they had already read it. Oh well. 

  7. What is a gene, post-ENCODE? History and updated definition (2007) Gerstein et al Genome Research [pdf]

    The ENCODE project, which was to go on to play a significant role in my life for a period, sparked more conversation than ever about regulatory genomics. This perspective article discusses the definition of a gene looking back over more than a century of scientific understanding. The conversation was continued as the ENCODE project unfolded – as discussed here at Nature News.

  8. Trisomy represses ApcMin-mediated tumours in mouse models of Down’s syndrome (2008) Sussan, Yang, Li, Ostrowski & Reeves Nature [journal link]

    When I applied for the place on the Imperial College PhD program (interview mentioned above) I also applied for a place on a similar program at Edinburgh. There, the interview involved presenting one of a choice of several papers, and this paper was one of the options. Being the precocious undergraduate I used to be, I had a subscription to the print edition (remember those?) of Nature at the time, a touching birthday gift from my grandfather. I had already read this paper and heard about it on the Nature podcast [link to transcript]. I emailed Reeves to clarify a couple of points which I had not understood from the paper, and we had a charming email exchange which I will tell you about in person on request. 

  9. Can the flow of medicines be improved? Fundamental pharmacokinetic and pharmacological principles toward improving Phase II survival (2012) Morgan et al Drug Discovery Today [pubmed link] and Lessons learned from the fate of AstraZeneca’s drug pipeline: a five-dimensional framework (2014) Cook et al Nature Reviews Drug Discovery [journal link]

    Since moving to industry I do not blog much about work. These two papers, referred to colloquially as the “three pillars” and “five pillars” papers, discuss just how hard it is to make a medicine.

  10. A reanalysis of mouse ENCODE comparative gene expression data [version 1; referees: 3 approved, 1 approved with reservations] (2015) Gilad Y and Mizrahi-Man O. F1000Research [doi link]

    A second mention for ENCODE, this paper was notable for the fact it addresses confounding (an important concept in design of experiment), its use of forensic bioinformatics (using file names to reconstruct the design of a study) and its unconventional route to publication via a reanalysis that was first shared on Twitter. The discussion thread on f1000 is worth a read. Zeitgeisty at the time. 

Happy reading, everybody. 

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Making real change happen

For those of my readers who are new to my writing, karibuni. Stay with me. The video is for the sake of nostalgia. I am going through a nostalgic phase at the moment.

It has been a while since I blogged a conference report. I remember, for example, live blogging Cromer is so Bracing ‘09. The output of that meeting may not have been Real Change Happening but CISB’09’s delegation did Make a short film about Darwin’s theories and their origins in Cromer, Norfolk, England, and not the Galapagos as we had assumed at the start of that meeting.

In present-day England, somewhat west of Cromer, and then North a little, for the period Wednesday 28 August to Sunday 3 September I was a delegate at ISPS Liverpool 2017. ISPS is The International Society for Psychological and Social Approaches to Psychosis and ISPS Liverpool 2017 is ISPS’s International Congress. The theme of the Congress for 2017 was Making Real Change Happen.

On the first day of the conference, Wednesday, I arrived in Liverpool in time for the drinks reception. I met a jetlagged Indian who had flown in from New Zealand. We went for Mezze together with some Liverpudlians whom she knew from a previous life.

Spot the Liverpool debutante.

Spot the Liverpool debutante.

The circumstances of my delegation were that I saw the Congress mentioned and thought it looked interesting. A delegate registration was transferred to me by someone who had registered but was unable to make it via a mutual person. On Thursday, the first full day of the Congress, I arrived to find that person, Rai Waddington, delivering a breathtaking keynote to a single cartoon projected behind her. No hiding behind endless Powerpoint slides for Rachel.

Alt text

Rai Waddington speaks to the Millenials in the audience.

During one of the subsequent parallel session I asked one of the speakers a question about the work he presented. My question was about the validity of the metric being used to measure one of the outcomes in his study. I was as gentle as I could be in my line of questioning and the reaction to my question was sufficiently strong that I felt awful. It dawned on that I may be the only Fellow of the Royal Statistical Society in attendance at ISPS Liverpool 2017.

Spot the statistician.

Spot the statistician.

A poetry workshop that took place on Thursday was the dowsing that located my tears. I used the back of my hand for ninety seconds and then ran to the toilets before my mascara got there. For this meeting more than any of those I have attended in the past the question of how a woman in academia was best to present herself hung over me. The importance of appearing kempt and the hours I was taking with selecting outfits, with ironing, with make up, how important to me it was not to be seen as one of them struck me. For all of the work that I have done on stigma I continue to fall at this authenticity hurdle.

The poem that Gill O'Halloran, Poet in Residence put together as a result of Thursday's poetry workshop.

The poem that Gill O’Halloran, Poet in Residence put together as a result of Thursday’s poetry workshop.

Liverpool felt at once homely and disorientating. I found refuge from the alienating architecture of the city centre in a two bed terraced AirBnB with my host Leila. Leila appeared dressed for Mosque on Friday morning and explained that it was Eid. She went on to regale me with an anecdote about a year spent lunching on rice pudding as a child after her father had declared to her school that she could eat nothing that had been cooked in the school kitchen. He had meant nothing that contains pork, but had omitted the “that contains pork” bit. Leila departed for Mosque and I set off for the second full day of the Congress.

One of the most valuable gems I have ever been gifted was given to me as part of the PhD process. It was advice pertaining to conferencing. Pick out the sessions that you really want to go to, attend those and spend the rest of the time sightseeing. With this in mind I took Friday afternoon off. I went to the Albert Docks and to Tate Liverpool and on the Wheel of Liverpool. I had an early night in mind but instead stayed up until two in the morning drinking cups of tea and trading stories with Leila.

A picture I drew when I was sat on the floor at Tate Liverpool. Charcoal on paper.

A picture I drew when I was sat on the floor at Tate Liverpool. Charcoal on paper.

On Saturday despite having slept little the night before I came in early with the aim of going to the session about students, because I love them. I learned about a student run project that is grappling with the idea of sustainability now that its student founders are graduating and getting real jobs.

Jana and Barbara led a workshop on how they are already making change happen by facilitating Czech psychology and medicine students volunteering in psychiatric institutions.

Jana and Barbara led a workshop on how they are already making change happen by facilitating Czech psychology and medicine students volunteering in psychiatric institutions.

On Sunday I said goodbye to Leila and listened to the closing speeches and worked on this blog post and swapped contact details and wished people whom I had met only a day or so earlier a safe onward journey. The ISPS International Congress is biennial. The 2019 meeting will take place in Rotterdam and had as its theme the question of whether and how cities send people psychotic. Something to think about. In the mean time here are some images that I drew with my SharpiesTM of the conference as it happened.

Maybe I would have found my BSc less stressful if I had sat in the lectures sketching the lecturers?

Everyone who works in Mental Health knows who Gail is according to Debra whom I met on Sunday. I get the sense that this might be an Australasian reference.

There was a conference choir. Of course there was. They drew the conference to a close by performing Stand By Me.

Following a rehearsal on Saturday, the conference choir drew the conference to a close on Sunday by performing Stand By Me.

When it comes to change, and to Making Real Change Happen, I have been told that change is the only constant and further that acknowledging this truism is the only way to stay sane. These aphorisms seem somewhat at odds with the theme of ISPS. In Making Real Change Happen at the societal level are we inducing collective insanity? Will there be anarchy? Would that be so terrible? Home Counties Anarchist is one way to describe me. Is the social movement I bore witness to at ISPS the noise or the signal? We have been round before with R. D. Laing in the 70s and that did not end terrifically so who knows where next. Regression to the mean perhaps? For all that the Congress was about Making Real Change Happen, what is my role here? Change happens anyway. My PhD taught me that prediction is devastatingly difficult. My PhD pertains to the topic of prediction in complex phenomena and I and cried a lot during my time as a postgraduate student. The properties of connectivity in complex systems and the inference of causality in those resultant networks are challenges sufficient for people I know to write papers on the properties of networks and Bioconductor packages on the inference of causality in systems so complex to be beyond our current understanding and none of us have the answers yet despite the amount of money and time and emotional energy that we are spending on ourselves and our coffees and our conferences and our fancy computers.

For me, for now, I plan to hold a steady course and stick to biochemistry, bioinformatics, computational biology, statistical genetics, statistics and statistical consulting. The world is small for the moment and I am your friendly local statistical consultant. When you are ready with your enquiry you are welcome to find me on your favourite social network.

Your friendly local statistical consultant.

Your friendly local statistical consultant.

With thanks to Rai, who got me the ticket, to Jens, the conference photographer, and to Leila for her kind hospitality.

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Erika, undergraduate edition.

Erika, undergraduate edition, with a fellow student.

I do love how I used to be as an undergraduate. During a clear out, I found an academic diary from the first year of my undergraduate studies.

Diary from first year of undergraduate studies.

Diary from first year of undergraduate studies.

In it, in the notes pages, in between a note about booking a coach travel ticket and a shopping list, is written the phrase “Cancerous tissue has deranged glucose catabolism”.

Cancerous tissue has deranged glucose catabolism.

Cancerous tissue has deranged glucose catabolism.

I have traced this phrase to a “More Medically Relevant Example” in Chapter 14 of Lehninger’s Principles of Biochemistry, fourth edition. I always did prefer Lehninger to Stryer.

© 2005, 2000, 1993, 1982 by W. H. Freeman and Company

© 2005, 2000, 1993, 1982 by W. H. Freeman and Company

Quite why I would have noted this phrase down in between a note to self about public transport options and a list of things to pick up at the supermarket I do not recall.

The photo at the top of this post is of a fellow student and me and was taken in second year, shortly before I hung up my lab coat.

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Commuting and communities

Biodiversity in Stevenage

Biodiversity in Stevenage
Stevenage, Hertfordshire

Crick's Corner, 80 Dartmouth Park Hill, London N19

Outpost of The Crick, closed Sundays after 1pm
80 Dartmouth Park Hill, London N19

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Self promotion

Self-promotion via Bad Science Jokes

via Bad Science Jokes

I do find the trope that women do not self-promote tiresome. If I self-promote, does this mean that I am not a woman? 😕

It is not in my nature to do disco moves in a lab, but I do admit to having done some stuff. However, when I talk about the stuff I have done, this does not always seem to go down so well.

I have been told I have a male brain, more times than I can count. (Aren’t male brains supposedly more numerate?). I get so cross with this. I do not have a male brain. I just have a brain, and a number of personality traits that are culturally coded male. I work as a statistician, so I am logical and analytical and even reductionist because it is my job to be logical and analytical and even reductionist.

I am empathetic and creative, and a friendly person, generally, and when I am a statistician-scientist I am in an analytical role, so when my recommendations based on your data appear to be unsympathetic to your scientific intuition, that is because I doing my job with integrity and not because I am callous. I like Bayesian thinking, but I do not, as a rule, account for hope – mine or yours – in the prior distribution when I analyse the data.

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Father’s Day

One of the few issues on which my parents both took the same, apparently unwavering and absolute position was that of the sanctity of the secret ballot. Vote, my father said. No vote, no voice, he said. People died for your right to vote, he said. If you don’t vote, he said, don’t complain.

Imagine my shock, then, during the 1997 United Kingdom General Election. My school staged a Mock Election. Sixth formers represented the different (Mock?) parties. Campaigning took place over the course of a week. To my memory, the Mock Green Party campaigned vociferously, and used green balloons; the Mock Tories campaigned barely at all.

On Mock Election Day, the School Library became the polling station. Library users were turfed out. For one day only, these were not study spaces but voting booths. I recall the whole exercise being undertaken with a sense of gravity, but that might just have been me, ever mindful that people had died for my right to vote.

I do not remember whether or not there was an exit poll.

Library desks became polling booths This image is of individual study areas at the University of Maryland's Engineering and Physical Sciences Library

Library desks became polling booths
This image is of individual study areas at the University of Maryland‘s Engineering and Physical Sciences Library

When the Mock Results were announced, the Mock Tories had won. If I remember rightly, despite campaigning the least of all the Mock parties, they won by a 75% majority. The announcement of the winning party was one of those coming-of-age moments. It dawned on me that my parents are, on certain matters, really quite different to other Surrey parents.

As regards the upcoming referendum, I watch Stephen grapple with both sides in a very public way. The CEO of my employer set out the position of the industry I work in, in a letter to the Observer. At that Mock Election nearly twenty years ago, I learned that not everyone applies the principle of the sanctity of the secret ballot in the same way that my parents do. I wonder, is there a word for that feeling when someone tells you, “I voted X, how about you?” and in that moment, your whole understanding of what is at stake becomes a fraction more blurry at the same time as you duck out of the debate, quietly, self-conscious about how supercilious you come across: “I believe in the sanctity of the secret ballot”.

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When in doubt, read the instructions

is to productivity

what aphorisms are

to meaning.

Went shopping for clothes. Came home with books. Story of my life.

My most-liked Facebook post of all time.

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Everything the light touches

Everything the light touches
Buda castle

Buda castle

Buda castle

Centennial Monument, Margit-sziget

Centennial Monument, Margit-sziget

Japanese Garden, Margit-sziget

Japanese Garden, Margit-sziget

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Birthdays on the brother blog

Contemplating Birthdays on the Beach

Contemplating Birthdays on the Beach

This week, I reviewed Having a Birthday as part of Ant Cule’s project antcule.reviews, (Subtitle: An Extremely Subjective View of Being A Human).

For the uninitiated, Ant and I collaborated on this blog post about giving a talk, back when I was a PhD student, more than three years ago now.

Ant welcomes requests and guest reviews, if you feel so inclined.

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MOOC review of Think Again: How to Reason and Argue

The Coursera course Think Again: How to Reason and Argue started again on Monday – there’s still time to sign up! I took the course in the second half of 2014, making me a Think Again alumnus. If you are looking to learn something new this new year, then Think Again could be the course for you. Read on for a review.

Reasoning is important, and Think Again promises to teach you how to do it well. I have blogged before about public speaking, and when I signed up for the course I had in mind that this course would help me to take my public speaking to a new level, beyond delivering information and into the realm of persuading and debating – having conviction and the courage to match. Whilst the course does indeed discuss

how to identify, analyse and evaluate arguments by other people including politicians, used car salesmen, and teachers

it stops short of turning you into one of those characters. This course was not about rhetoric per se. It was about the logic underlying arguments, about how arguments are constructed and deconstructed, and how to identify and evaluate arguments – what makes a good argument? The course had connections to linguistics, logic, and, yes, statistics.

Course teachers Walter and Ram

Course teachers Walter and Ram

The course was taught by Walter Sinnott-Armstrong, Chauncey Stillman Professor of Practical Ethics in the Department of Philosophy and the Kenan Institute for Ethics at Duke University, and Ram Neta, Professor of Philosophy at the University of North Carolina at Chapel Hill. Professor Sinnott-Armstrong is co-author (with Robert Fogelin) of the course textbook Understanding Arguments: An Introduction to Informal Logic. Walter and Ram present the course as a humorous double-act, Walter’s clownish humour alternating with Ram’s deadpan wit.

The course textbook

The course textbook



The course was twelve weeks long, structured as four three-week long units, taught alternately by Walter and Ram. The course material was delivered each week as a series of bite-sized lectures. Students could check their understanding using multiple-choice exercises that follow each lecture, and read the accompanying chapters in the course textbook. Online discussion forums on the Coursera website enabled students to check their understanding and clear up misunderstandings – and to help fellow students to do the same. At the end of each three-week long unit was a graded quiz, and if you achieve an average grade of 70 or above on the four quizzes you will receive a Statement of Accomplishment signed by the professors. An average grade of 85 or above will get you a Statement of Accomplishment With Distinction also signed by the professors!

An outline of the course syllabus is given on the Coursera website, and you could get a more detailed idea about what is covered in the course by looking at the table of contents for the course textbook. Key learnings from the course include one from the very first week:

An argument is not a verbal fight

Useful to remember if a difference of opinion gets heated, online or off. I studied truth tables, the difference between deductive and inductive arguments, and logical fallacies. When I was not studying, it was fun to spot, uniting and reconstruct arguments in everyday life. Or, fun for me at least – I mused out loud that this Coursera course was changing the way I think, only for my husband to retort that it was making me “really annoying”. Oops.

Some students on the course – Courserians as we are known – went further than just observing the structure of arguments in their everyday lives We were encouraged by the course teachers to upload our own arguments to the discussion forums, and to comment on the arguments uploaded by other students. Some students created their own short videos to illustrate the course material, and a few of these videos were incorporated into future editions of the course.

This was my second run at a MOOC – earlier in the year I took Statistical Learning, also starting again soon, at Stanford Online. I learned from that first MOOC experience and when I took TA:HTRAA I made more of a conscious effort to set aside the time to study. A MOOC, with its lack of lecture theatre or exam hall, requires a different sort of commitment compared to bricks-and-mortar study. It can be challenging for students to set aside the time each week. One student in the discussion forums suggested watching the videos twice to aid understanding – a great idea but of course taking twice as much time. I used the Coursera app to download the video lectures, and studied on my commute, with a few binge-studying sessions to catch up on weekends.

I would recommend Think Again: How to Reason and Argue to people working or studying in a wide range of fields. Regardless your day job, the information, tools and techniques taught in the course will help you to reason in everyday life. If you would like to stretch your mind an a different direction this year, or are considering taking a MOOC perhaps for the first time, then signing up to Think Again would be a great move! And, if you do not agree with my endorsement, I would be interested to hear your counter argument.

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