John Jackson OBE (1934 – 2023)

It is good to read about a life well-lived, I think. Especially if you struggle with your own existential dread. (Following Covid, isn’t that all of us, to a degree?)

My mother’s Uncle, John, to us “Uncle John” even though he was actually Great Uncle John, died last month. The funeral will take place next week. It’s a sobering moment for us as a family, because John represents the last living blood relative of my grandparents’ generation on both sides. John leaves behind his second wife, Pat, his two sons and my mother’s two cousins Alistair and Andrew and their families, an enormous number of lives touched, and, well, us. Me.

John Jackson RIP

I cribbed this picture from the Burton Albion FC website. I hope they don’t mind.

I got to know John a little in his retirement, my adulthood. Before that he was someone we went to a football match with one time and a face in family photographs from a time before I have memories. But following the death of my grandfather George, John’s brother, J and I would stop by John and his wife Margaret’s place in the midlands on the way to or from the Lake District. After George and my other remaining grandparents died in rapid succession within a matter of months in the early 2010s, my whole immediate family gravitated towards our parents’ and grandparents’ siblings, as if putting out tendrils, desperate to connect to what remains of each other here on Earth. Redoubling our efforts with more obscure branches of our family trees.

Family photo from 1988

Family photo circa 1988

I knew little of John’s life before he retired, I only read about it just now in two articles in the local press.

I had known that John was active with Burton Albion FC, his local football club, and involved in its work in the community. I hadn’t known, although it doesn’t surprise me to learn, that through his previous role with Burton Albion Community Trust he had been instrumental in enabling the Pirelli Stadium to become a vaccination centre during the pandemic. Our whole family is quite “light under a bushel”, I am perhaps less this way inclined personally but in general it is in our family culture to be understated.

I knew John for his warm hospitality, his unlikely fandom for Russell Brand, the sincerity with which he welcomed us as a newly married couple and with which he talked with me over the years as we grappled as a family with our history and with our future. I remember how he took his own tragedy and worked with his son to make a BBC Documentary on a systematic problem in UK Hospitals, always with care and love and never with self-pity. His late wife Margaret was an astonishing character, and following her death John never wallowed but carried on, welcoming J and I, holding my hand when the marriage failed, building relationships and being at the centre of his community.

I know John’s death isn’t about me, but he won’t mind being part of something bigger – that was him in life for sure. I want to note somehow how different birth and death look once one believes. When John was dying, I felt calm and steady; I prayed because that’s what I do now, and I listened to others grieving and grappling. Coincidentally seeing as it’s John’s funeral this week I held a newborn for the first time in several years too, the much-longed-for son of a friend; I gazed into its unseeing eyes, my heart unable to hold onto this miracle. Babies are have been Simply Marvellous, but Everything Is Different Now.

Lots of love to John and his family, and blessings aplenty to my new friend’s new life, also, as it happens, a “J”.

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I am evangelical about this

PhD students should* consider industry roles; academics should not dissuade them.

Ten years ago today I began my career as a statistical consultant in the pharmaceutical industry. I went directly from my PhD: I submitted my PhD thesis on a Friday, went clothes shopping on the Saturday and started my new job on the Monday. I moved house the following Thursday, in order to cut my commute down by the order of one cross-London Tube journey.

Academia, and academics, can be hostile to this sort of hijinks. After I left Imperial and UCL and went to industry, I missed academia. In the intervening years I negotiated my own time with my employer, enabling my attendance at numerous seminars, workshops and other academic events related more or less tangentially to my day job. For me this was not related to career progression, nor what industry calls technical development. This was a different sort of outlet, a form of nostalgia. I would turn up and listen, wanting a sense of homecoming, only to realise I am overdressed, too direct with my language, and did not belong at all in those dusty lecture halls anymore.

Erika with the GSK pride group ready for the parade to start in 2016.

A statistician who has never felt more awkward: the one time I relented and put on a company-branded T-shirt, at London Pride in 2016.

In corporate life, one was supposed to carefully plan one’s conference attendance for the year during January, jointly with one’s line manager, but I was line managed two layers up from the US. Because time zones I could get away with going to various extra-curricular things during work time, in London, usually, especially if I could find a quiet corner of a conference to dial into any important meetings. Don’t get the wrong impression of working industry life: whilst the work-life balance is, in general, compared to academia, more reasonable, it varies over time and career stage as it does in any profession. The flexibility I was granted with my working hours is by no means a given. I earned trust through the Seattle gig among others, ask me in the pub about that and I’ll tell you. I could turn the handle when needed and hated letting colleagues down; to the extent that I was able, I delivered due work to timelines.

Industry suits some people better. In concrete terms: academia is a zero-sum game. I get the grant, you do not get it. I scoop you, I get the kudos. There are finite prizes, and limited resources. Fighting for academic karma points becomes one’s raison d’etre. I am reminded of Sayre’s law as applied to academia in a quotation usually attributed to Kissinger and rephrased to me as

In academia, the fights are so bitter because the stakes are so low.

I am not saying this is a bad thing. It’s not even true quite a lot of the time, for all that it is quotable. Academia suits some people, seems to let many more of them down, and does not suit some others.

In research in industry, the stakes are not better, nor necessarily higher, so much as they are different. The whole ship is at stake; if one of us goes down, we take others with us. Humans are still humans and whilst turf wars and latent power struggles and empire building and all the rest of it do go on, the overall winners are not always the ones who fought to be first author. The goal such as there is one is to navigate the whole team through current, concurrent economic, scientific and political cycles safely, with the minimium of carnage, and, in pharma, hopefully along the way to play our incremental parts in the process of making a medicine. One goes from being master of one’s destiny with an outcome to an extent proportionate to time spent at work, to a tiny, tiny cog in a hundred-thousand person machine. There are roles for everything, including things that you have never heard of. So I was the statistician who supported the pre-clinical scientists in one or more areas of biology, or one or more technologies; at one point I was the in-house go-to person for the statistical design of transcriptomic studies; another the stats point person to Immunology. A niche within a niche, as it were, but I was perceived to add value nonetheless. If this had not been the case, my role would have been made redundant eventually.

Corporate adjustment is the change in ways of being and doing from academia to industry. It hurts. An academia to industry career transition needs to be made judiciously and with a degree of self awareness. The move is easiest at one of two career stages. One can move, as I did, fresh from a masters or doctorate or perhaps a short postdoc just to make sure one was not at home in academia. At this stage one is malleable, still relatively young and able to learn new things quickly, and not yet quite so wedded to the ideals so important mid-career. The other people who arrived who were successful were professor-level and brought something specific. In my field this was usually technical expertise. If these people came willingly they commanded respect straight away, especially if they were known from the literature and conference circuit.

To conclude: students, think of industry as a realistic career option; academics: your colleagues and counterparts in industry know things you do not. A collaborative and healthy working relationship between academia and industry is a beautiful thing, the best of both worlds, and a joy to be a statistical consultant to. Those roles are some of my greatest pleasures.

Have fun, y’all.

* I don’t really believe in “should”, said breezily with a wave of the hand, used to be one of my maxims. My vocational transition is about as much fun as it sounds.

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Computers these days

When I was in primary school, in the early nineties, Tesco ran a scheme called Computers for Schools. Shopping at Tesco earned paper vouchers which were collected by local schools. When a school had collected enough vouchers, they could spend them on computer equipment.

The window of time when I was in love with technology began when I was five or six years old. My primary school employed the father of one of the kids to teach us the basics on the suite of Acorn computers my school had bought using Tesco vouchers.

The IT teacher taught us two maxims:

  1. It is very difficult to break a computer, aside from using a hammer. This teaching was designed to encourage us, as we learned the rudiments of BBC Basic or word processing, to experiment, to wonder what this button does.
  2. Computers are stupid. They do what humans tell them, and nothing else. If someone’s machine did something unexpected and the teacher was called to investigate, the whole class would carry out a call-and-response exercise:

Mr IT: Computers are…?

Class: Stupid!

I progressed from Acorn computers to Windows. At home we always had a modern PC, cast off from my father’s place of work. Their tech was being upgraded annually to keep up with the demand of that field. I remember vividly the day dad came home and told us kids solemnly that this new computer had a gigabyte of memory.

Wow, Dad.

I said.

What’s a gigabyte?

In preparation for my undergraduate studies, I pored over PC World magazine before picking out a Dell desktop, a gift from my father. I took immense care of it, and used to open up the case to add RAM, virus-check it often, and back up my work to a series of DVDs every month(!). At the start of my MSc I won a MacBook in the essay escapade and became a Mac convert; I worked primarily across UNIX and Mac for the next four years. As well as the trusty MacBook I was furnished with a beautiful 27-inch iMac and a UNIX box with NVIDIA GPUs for my PhD, with thanks to the Wellcome Trust for their generous funding. Further I had access to Imperial’s incredible High Performance Computing service for anything my own tech could not handle – quite the privilege.

On my first day in my first job post-PhD, the hiring manger handed me a laptop with the apology that it ran Windows 7, meaning that the company’s Windows 8 upgrade was still in progress. I replied dryly that I was sorry that it was Windows at all, perhaps the first indication that corporate Erika was not going to be an authentic edition of the self. I installed emacs to do my work in R, and got hauled up by IT whose virus-scanner had picked up one of the extensions I had installed, which makes emacs keybindings work in Microsoft applications and reads to a virus scanner as a keylogger. Oops.

Working with corporate IT is different to working with academic tech, where I had been largely left to my own devices. As the years passed I came to learn that it was in my best interests to get on with the job in hand, and that it was not my job to try to understand what was going on under the IT hood. Outside of work, I had a succession of iGadgets and was aware that I was becoming less and less au fait with how the whole thing chained together.

But it’s not just me. Richard once told me “you have tech chops” and that is probably still true to an extent, but I don’t think Maxim Two holds anymore. iGadgets and their ilk now hoover data up furiously. Behind your back they mine email, social media, calendar, text messages and photos. Your friends end up tagged, your geography monitored, memories and suggestions are supplied to you unbidden. If you have had a turbulent few years involving the loss of the husband, marriage, home, career and worldview that you once treasured, this is a cruel system, worse than human memory that can blindside you with a once-familiar perfume or train station, say. No, I do not want to see a photograph of my honeymoon today, thank you very much.

That window of time has closed, then. Yet another important aspect of my life that my perspective has changed on. Weird.

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Darwin and the divine

On Boxing Day, Jerry Coyne posted his blog post The New York Times touts religious miracles as proof of God. In his post, Coyne deconstructs an essay published in the New York Times. The essay by Molly Worthern uses individual testimony as the source material and contemplates the question How would you prove that God performed a Miracle?

Coyle says:

Worthen’s title question mentions two important issues. First is that of “proof”, which is really irrelevant to a scientist since we don’t think of empirical “proof” of God—or of anything. We speak of the strength of evidence, which, to me, is strong for the formula of a water molecule having two hydrogens and one oxygen, and far, far weaker for an omniscient and omnipotent being who cares for each one of us.

Coyle says that scientists do not think of empirical proof of anything, which might be true in theory. However, Coyle’s retirement is showing. When a laboratory scientist consults me in my role as project statistician, their project is grounded in the truths of their discipline. Accepted theories allow next experiments to happen. In designing an experiment, we control for the less certain truths but we don’t, for example, let the theory of evolution by natural selection be taken as less than a truth for the sake of our experiments, just because, per Coyle, we cannot consider it to be proven empirically.

What I am getting at is that the scientist at the coalface knows of truth in two senses. They know the truths of their day, theory-as-accepted, language with which to share new findings with colleagues. To an outsider watching the work, this information appears to be certain to everyone involved. The true scientist, though, also holds in her heart that at some stage in the future, current truths might become past theories as new information emerges. A scientist who cannot work with this paradox becomes frustrated and stuck.

Erika competes in the backstroke at the Cold Water Swimming Championships, 2015.

Erika competes in the backstroke at the UK Cold Water Swimming Championships, 2015.

The reference made to the molecular formula of water pierces me in a way that it would not have before. It is the very existence of the water molecule, with its atoms and its properties perfectly in tune with the demands of photosynthesis, respiration, death and renewal, that serve as the evidence of existence of something divine. Long before I became a Christian, I for several years swam round the year outdoors, so central to my well-being. Simple immersion connected me with the changing seasons. Central London life can bypass the rhythm of the year; ice, frost, algae, blossom then crowds, weeds, dying leaves into the ice again were the way I kept in tune. It does not surprise me that much in hindsight that I was unable to thrive absent this ritual and broke down in a life of corporate tyranny and commutes.

Water is symbolic for Christians via baptism; there is holiness also in the making and sharing of a cup of tea. Discernment seems to involve a lot of tea.

I don’t have any particular authority in the faith/science pseudo-divide. I find the conversation boring quite frankly, a bit of a wankfest. Is the earth 6,000 years old or four billion? I don’t care, I’m not a geologist.

Admittedly the evolution by natural selection piece speaks to me more; I cannot not be a Darwinist however hard I try. But I believe that I understand probability theory, why the scientist’s spirit is drawn to the significance test, and what those pesky p-values really mean. I look at all of that, and I look at my soul and its longing. I picture the cygnets and swans on the Serpentine this coming spring. I contemplate the journey ahead. Integrating all of that in both sense of the word, I found my belief in God. I went with Christianity for the simple reason that I was baptised as an infant. My journey began itself around me, before I joined alongside.

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Do one day at a time.
If you can’t do a day at a time, do an hour at a time.
If you can’t do an hour at a time, go minute by minute.
If you can’t do minutes, do seconds.
If you can’t do seconds, do moments.
Do moments, all you have to do is moments. Just keep breathing.

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What is it like to go dating for the first time?

In the video, I explore what it is like to go dating for the first time.

With thanks to Kate Smurthwaite (who introduces me here and who taught me stand-up comedy), City Academy (through whom I took this course) and The Comedy Pub (where we performed).

Thanks to my friends and family who attended and/or helped me to write the jokes. Most of all, thanks to the Funny Sckool Graduates (you know who you are).

Lastly, thanks must go to my First Husband for giving me this opportunity.

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Making it up as I go along

Until recently, I dreaded public speaking. Hated it, even. No-one told me, when I set out to become a scientist, that presenting my work in front of an audience would be expected. Being scheduled to give a talk, to immediate colleagues or to a conference audience, could ruin the day if not the entire conference. I still get anxious now, but I am not so disabled. I have a greater capacity to handle the unexpected.

This performance problem started to bother me seriously when my coping strategies began to hold me back. I had developed the habit of cutting a deal with collaborators: I’ll write the slides, if you present them. I do myself a disservice this way, because no one remembers my name in the acknowledgements section. Science loses, too, because sometimes I do not have a collaborator to hand, so my work stays in the shadows. Science only works if we share it.

I was frustrated. I had to fix this. Coaching, mentoring, taking courses, blogging, and reading books on the topic had brought me to a stage where I was able to bear it. Feedback on my most recent presentation was that it was fine, and maybe it was, but I had skipped the morning conference session to worry over my slides and spent lunchtime wondering where I could get hold of a whiskey to steady my nerves. The relief once the thing was over was so great that I remember nothing of the closing plenary. 

At this point, I saw two options: Toastmasters, or Improv. Toastmasters sounds dire. I added “Take an Improv class” to my to-do list. Last summer, one sleepless night in the wake of my marriage, several crises, and a house move, I thought “fuck this” and signed up for Level 1: Beginners Improv Course.

Gregarious friends commented on my courage when they heard what I had signed up for; a colleague remarked, when I confessed, several weeks in, “that’s going to make you a nightmare!” The thing is, I am alright with small groups – I like leading those. Hundred-person auditoria, though, with my work and hence me under scrutiny, make me panic. Improv was hard. Really, really hard. Statistics benefits from a thoughtful approach, one of the reasons I like it; some of my favourite blog posts are the most considered ones. Kudos, then, to Steve, who put a lot of work into making the studio a safe space for all of his students. I can forgive him for that one time he made me Improv statistical consulting.

Every Wednesday night after work, for eight weeks, getting to class meant some sort of mad scramble: a bus, two trains, a Diet Coke and a takeaway dinner. I would screech to a momentary halt in a theatre space above a bar in Moorgate. The door would shut on our Studio, and something would shift. Adulthood, and the news, and the turmoil I am fighting to heal from, would, somehow, be suspended. There is a distracting effortlessness about Improv which consumed all of my concentration. Within moments I would be crying with laughter over bizarre drama games. My dozen course mates and I stretched, swung our arms and swung each other around, sang, danced, crawled, and improvised our way through couples’ counselling, a cocktail party, a film set, and a flight to the moon. All in one evening, some weeks. Outside of class, we formed a WhatsApp group, a pub night, each others’ party guests; the following term, some of us were the loyal audience whilst others went on to perform. Improv was exhilarating, enriching, exhausting. I used to come home buzzing and unable to sleep until midnight. 

And, did it work? 

Erika and her Improv colleagues

Improv classmates with our tutor, Steve. And some Oreos.

Halfway through, I got offered a no-notice trip to Paris – a colleague pulled out of a conference at the last minute. I do not like travelling – it always feels taboo to admit that – and short-notice travel causes me particular problems. There I was, then, blinking at my boss’ suggestion. I’d just come back from a weekend away, as it happened, and here I was facing going abroad a day and a half later. I froze, processing how fast I would be able to turnaround my laundry from the weekend, and which meetings I could miss and which I would reschedule, and where was my passport, was there any chance it had gotten lost in the house move? I tried, and I tried, to find a reason why I should not take this opportunity. Then, I remembered the first rule of Improv. 36 hours later, I was being woken up at Gare du Nord by the security guard sweeping the Eurostar. Unsurprisingly, given the weekly mad scramble, the laundry that I had done through the night whilst I searched for my passport, then the day at the office, back to back, of course, with rescheduled meetings, I had fallen asleep on the train. 

Paris is not presenting, but when travelling, as when talking in public, you can plan all you like, and still know that you will be thrown a few curveballs. I’ll tell you about Paris, one day, if you ask me. I have presented since (in fact twice in one afternoon, once). So, I would say: Yes. It worked.

I took Level 1: Beginners Improv Course with Hoopla.

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The New Awkward

Ah you see, this vulnerability-plus-authenticity-thing, it’s a new skill I learned recently. It’s only awkward if you make it so*.

I LOVE the vulnerability + authenticity thing! I'm for making anything that isn't this, the new awkward. WhatsApp. It’s like Twitter, but better curated.

Blogging lends itself to the meta.

Over the years, when I have been battered, bruised and even left bleeding from online exchanges, I think back to my abrupt and unintentional induction into science communication; to my first forays into blogging. I finger the battle scars I picked up during the Science Blogging Warz of the late 2000s, I switch off for a while, I step away from the internets, I rethink, I rephrase things. We all go to the pub, sometimes, and that helps a lot.

Kids: be loyal to your friends, and your internet strangers; stay connected to your networks even when they disconnect you; be disloyal to platforms, to frameworks, to media. Think carefully, before thinking absolutely. Be the person organising the watch party, the fringe event, the Tweetup. Don’t piss on each others’ carpets. Stop spitting bile at the universe from behind your safety glass screen. When the opportunity arises, make time to meet in up meatspace instead.

In 2013, almost invisibly, Blogging the PhD rolled into Blogging Beyond. Offline, I was enduring yet another interdisciplinary transition: from biostatistics student to industry statistician As this process unfolded, I no longer knew how to blog. I did feel the loss. Blogging about work seemed unwise. I tried and then tired of the diversity conversation. I posted photos. I cross-posted. For months at a stretch, I posted nothing at all.

Four years after that, and three or so since this, J called time on our marriage. It was not the first thing I asked him, but I did ask him, if he minded my blogging about it. My story is mine to tell, and his is his, and it is a pet hate of mine, having my story told for me. But from when J and I met in 2005 through to 2017 when our paths separated, our stories, from time to time, wrote each other.

There are so many what-ifs and wonderings: What if I had taken his name? Worn white at the wedding? Taken up the offer to do my PhD in Edinburgh? Explored the suggestion I move to Seattle?

dedicated my thesis to J, who, I remind him, will always have been my First Husband. I am not sure I would have made it to the start line of the PhD process, let alone the finish, without him. That said, looking back, I do question the wisdom of the caption of the photograph of us signing the register. I was trying to be funny.

C-x C-s , J
C-x C-c

The exchange at the top of this blog post comes from me (on the right) and Alicia Thackrar, with permission.

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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) Rosenhan Science [pdf]

    Often referred to simply as the Rosenhan 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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