Stories and Atoms

In artibus et scientiis, tanquam in metalli fodinis, omnia novis operibus et ulterioribus progressibus circumstrepere debent

Is this thing on?

tap tap feedback screech

Did you miss me?

To be honest, I didn’t miss me; I’d nearly forgotten that I had this WordPress instance running.  It’s been kicking its heels patiently for three years.

Three years.

That’s two elephant pregnancies.  Or thirty-something White House cabinet members.

I just reread the last post I made in 2016.  A lot has happened since then.  I’m not going to rehash the big stuff — Brexit, Trump etc — anyone who’s not been locked away in an isolation unit is aware of the shitshow playing out on both sides of the North Atlantic.

No, I’m going to focus on the personal instead.

And if you don’t like that, then what the hell are you doing browsing a website whose URL is basically just my name?  I suggest you go here instead.


 

If you’re still with me, thank you.  If you’re a Garfield fan who’s conflicted, stay with me for now.  God knows, I need the company more than Jon needs a punch in the face.


 

I’m coming up to my sixth anniversary working at Natera, and I’m still helping laboratory partners roll out our genetic-test-as-a-service concept.  I don’t think I’m allowed to tell you how many we have now, but it’s lots, with more coming.  I’m hugely happy to be working remotely on some cool biostatistics software, and I get to travel to interesting places once in a while (I’ve been to partner labs in France, Italy, Germany, Czech Republic, Romania, Spain, the UK, and South Africa since the last post in March 2016, as well as five trips back to HQ in California — and it looks like there might be a trip to Taiwan, Italy again, and Brazil this year).  It’s just enough traveling to be fun, but not too much to be a chore.


I was lucky enough to be able to sublet a friend’s room in May 2016, just for a month while he was away studying ceramics in Morocco (he’s an amazing artist, check out his IG account).  I used that month to look for a more permanent place to live.  I started off looking in Copenhagen, and found a place on Amager for about 8,000 Danish Kroner per month.  It was a two room apartment, with no garden, and a bit run down.  The landlord seemed nice enough, and I provisionally agreed to move in (I didn’t sign anything, though).  But I kept looking anyway.  My search took me further and further from Copenhagen — I looked at properties on Lolland and Falster, and towards the west coast of Sjælland, for example.  I looked at a nice property in a town called Reersø, but it was only for six months while the elderly occupants went sailing down on the south coast of France for the summer.  There was one more property lined up to see, though, about 5km from Reersø.  I nearly didn’t go — I was kind of depressed, and it had been a long day of seeing not-quite-suitable properties.  But it was basically on my way back to Copenhagen, so I went to look at it anyway.

It was a funny little place, on its own on a slight rise overlooking a lake called Tissø, with farmland and small coppices all around it.  The house was two bedrooms, one not much larger than a walk-in closet, and one fairly large living room.  It had a nice garden, a cherry orchard, and a garage/workshop where the oil-fired boiler lived.

The biggest surprise, however, was that the landlord was an old work colleague from my first job in Denmark at Leo Pharma in Ballerup.  So I figured, why not? And signed the contract.  I moved in on June 1st 2016.

Here’s a picture.

And I lived there, quite happily, for just over two years until I was burgled one evening in July 2018 while I was away in Copenhagen.  They didn’t take much — small electronic stuff and loose cash, mainly — but the sense of violation was considerable.  Stupidly, I had assumed that rural Denmark was immune from petty crime, so I hadn’t fitted any window locks or alarms (they got in by jemmying open a rear window).

Adam, the landlord, was sympathetic, and mentioned that there was an empty property right next to theirs that was basically the same price (higher rent, but heating was included), but it was almost three times the size.  He’d approached me about it the year before, when the contract was up for renewal, but I was happily ensconced in my tiny house at that time, and turned it down.

I was unhappy to lose my isolation, my view, and my cherry orchard, but the idea of being so isolated was no longer quite as appealing, and when I saw the new place, I fell in love with it.  So I moved in on August 1st, 2018.

It’s part of an old farm which has its own Danish Wikipedia page.  The history of the place goes back to 1350.  It’s a remarkable experience living here.  I’m still getting used to the space, but every day, with each picture I put up on the wall, and with every potted plant I buy, it feels more and more like home.


Other things have happened.

My father died in December 2017.  I turned 50 in October 2018 (and did a crazy road trip to Morocco, Spain, Portugal and Belgium with my friend Carrie).  I’m still single-ish.  My right knee is acting up.  I stopped doing the Charlie’s Bar pub quiz just under a year ago (it was eating up more and more of my time).


 

I got back from Spain on Thursday night, visiting my lovely, but increasingly dotty, mum and stepdad.

They’re doing OK — sort of — but stepdad, while doing extraordinarily well for a man of 88 summers — is inevitably a little unsteady on his feet.  He falls over distressingly often.  A couple of months ago, he fell while visiting the post office, right on his face.  Fortunately, he didn’t break anything, but did give himself two black eyes and busted his nose open.  I can’t look at the photos my mum took, they distress me too much.  He fell again while we were in town, this time without hurting himself (other than banging his knee a bit).  On the plus side, he has virtually all of his mental faculties, and his eyesight & hearing are excellent, and he still eats like a horse, even though he’s tiny.

Mum is well, although she’s aware that she’s not as mentally acute as she once was (and she once had a mind like a scalpel, so she’s still sharp).  She gets frustrated with stepdad’s inevitable mental lapses (reminder: he’s 88), and she is a woman of basically zero patience.  During my latest visit, she was considerably more stressed than I have seen her before.  I feel that her constant worrying about stepdad, plus her insistence on being in charge of every aspect of their existence, is becoming too much for her.  Getting her to do something about it, however, is another story. After a few gin & tonics, rational discussion becomes impossible, and she really just wants to vent.  So you have to let the storm blow over, which is difficult for me, having inherited her zero patience and considerable aptitude for temper tantrums.

I’m planning on going back there, post-Brexit (whatever that may be), and I think we need to talk seriously about making changes.  They have paid help once per week, and the Spanish neighbour has basically adopted them, but I think I might end up having to move to Spain (at least part of the year) to help them out.  Alternatively, they’d be welcome to move in with me.

Brexit, of course, could end up fucking that up completely, and we’ll all have to move back to the UK.  Let’s see what flavour of shite comes spewing out of the Parliamentary sewage system on Monday, straight from the Prime Minister’s bumhole, anyway.


And on that fragrant note, I think I’ll draw this missive to an end.

It you made it this far, pat yourself on the back.  Your capacity for boredom is considerable.

Why not reward yourself with some excitement by checking out the latest Garfield cartoon?

Travelogue

I’ve booked tickets over Easter for a quick trip to the folks before I leave for California for April. I can’t believe I was last over there nearly two months ago for stepdad’s 85th. Where does the time go?!  I was going to hold off until I’d heard from some of my customers, who have made noises about me coming to visit them, but I really don’t want to leave off seeing the folks for another month.  If I went over there in early May, that would have been nearly three and a half months since I saw them — too long.
 
So it’s nearly time to start arranging to move out of my friend Ole‘s place, which has been my home for these last seven months while he’s been touring Australia and New Zealand. I can’t believe I’ve nearly been in Denmark for a year already (that would be on April 9th). Next week, I’m going to book a storage unit and hire a man with a van to take stuff away a few days before I head off to Spain, and then I can get the cleaning done.
 
I’m back in the office in California for a couple of weeks at the beginning of April — it’s going to be so nice to see my colleagues again — then I’m going to take a fortnight off and go and see friends and family and just generally be badly behaved for a while up in Mendocino and in SF and Humboldt County.
 
Then it’s back to DK and the search for a new place to live starts again. I’m torn between getting a larger, cheaper place out in the country, and getting something smaller and pricier in Copenhagen. I’ve seen places for rent out in the country that are basically run down farmhouses for 5,000 DKK per month, with workshops and acres of land, which could be fun. It’d be more fun if I owned the place, but that’s not going to happen just yet, not until our company share price goes up a bit higher …
 
I can have a good think over April, and hopefully I can get something sorted out fairly quickly when I get back. I’m booking a room at Hotel 27 for a week at the beginning of May anyway, just to be on the safe side.
 
Being in Spain over Easter does mean I won’t be available for the March Charlie’s Bar pub quiz, but I’m beginning to doubt the wisdom of scheduling it for Easter Sunday, anyway. I’ll still get it prepped, and I have an understudy who has said they’d be happy to do the quiz itself, if needed.

Like An Old Cheese

CHEESE

If Java was a human being, it would be old enough this year, at the age of 21, to go and get itself shit-faced in a bar.

I first came across it while working at a financial tech company run by some former colleagues of mine from a previous financial tech company. We wrote an applet which pulled exchange rates from Telerate and showed them on a map. It looked pretty, but took forever to build, took ages to download over a dialup modem, and ran like a one-legged dog in Netscape. I wasn’t impressed.

I kind of ignored it through the late 90s, sticking instead with Delphi. I tried working with Java in Eclipse, briefly, around the early 2000s, and I still wasn’t very impressed. So I made Delphi keep doing things it wasn’t really cut out for, like an elderly horse forced to run steeplechases, and then I abandoned it in a field somewhere, metaphorically speaking, around 2007.

I knocked around with a dodgy crowd (PHP, Python, Perl, mainly) until 2013, when chance took me back to Java again.

And what a difference. JIT technology combined with processor speedups had made it almost as fast as compiled C in many cases. And the compiler itself was impressively speedy, too. A whole ecosystem of cool things had sprung up around Java itself and the JVM — a whole host of domain-specific languages like Groovy and Scala, for example.

I’ve spent the last three years catching up. I’m finishing up a project which uses Vaadin for the front end, talks to a mySQL DB through Hibernate, calls into a bunch of REST APIs to manage some jobs in the cloud, and generally uses some nice Java features that I was more or less ignorant of three years ago. It’s not finished yet, but I’m really pleased that I’ve been able to make as much progress as I have over the last couple of weeks. I mean, the thing has the feel of a proper product. I’m happy with it.

And I’m happy with myself for being able to learn some fun new stuff. My relationship with writing software hasn’t always been a great one — it’s always been a means to an end for me. But the tools that come as standard now — intelligent IDEs, fast compilers, source control, issue management, continuous integration — make it so easy to get up to speed.

Back in the day, we had to do all that stuff ourselves (and I’ve been doing this for money for 30 years now). And it uniformly sucked, with as much time being spent on maintaining the toolbase as we spent on writing the code itself. Having that support really makes a difference.  I’ve actually enjoyed doing this project.

Living in the future doesn’t suck some times.

Cheers, Java.

Concerns

poem

She regards her pale reflection
As it turns this way and that
In the dark, dusty attic mirror
Should she wear a different hat?
Will he notice her new outfit?
She smiles a little at that

She wonders at the weather
It’s still most beastly cold
Spring is just beginning
And the winter feels old
She decides to take a brolly
She’ll carry it neatly rolled

Are her stocking seams in line?
Are her shoes polished and neat?
She knows they’re last year’s fashion
Not comfortable on the feet
And will he stand and greet her?
And move to get her seat?

Her preparation takes ages
Slowly allaying her fears
A strangely old-fashioned young woman
An appointment that never draws near
Time itself is reluctant to say:
“You’ve been dead these seventy years”

She regards her pale reflection
As it turns this way and that
In the dark, dusty attic mirror
Should she wear a different hat?
Will he notice her new outfit?
She smiles a little at that

Image from Wikipedia

Predictive Models and the Life Sciences

Derek Lowe over at In the Pipeline (which I would unhesitatingly recommend to read if you’re remotely interested in how medicinal chemistry happens) discusses a new paper which addresses some of the systemic issues in drug discovery, namely the inconsistent use of predictive models (PMs) for making decisions about how drugs proceed through the discovery pipeline.

A big chunk of the problem is that drug companies look to diseases with no effective treatments, but part of the reason why no effective treatments exist is because the models of the disease are poorly constructed or just even plain wrong (because biology).  One of the big culprits here is Alzheimer’s, the mechanism of which is still not well understood, but that doesn’t stop Eli Lilly (for example) throwing billions of dollars at it in the hope that something will stick (spoiler: it probably won’t).

I’m familiar with the drug discovery industry: I spent 10 years developing and working with chemical informatics (cheminformatics) tools to support research chemists who were working in precisely this muddy world.

But since 2010, I’ve been working in the world of genetic testing which, for a variety of reasons, seems to have been able to deal with the issue of getting their PMs right a lot better than their cousins in the pharmaceutical industry.  This is partly because in genetic testing, you’re not looking for a cure; you’re looking for a genetic signal that strongly correlates with a disease state which in the world of high-throughput DNA sequencing is almost trivial to do.  The hard part is, as always, getting enough statistical support for your model from independent clinical trials.

It’s interesting to see discussions of PPVs and NPVs from the perspective of the drug discovery model, though, and I think this paper is going to end up being cited almost as much as Lipinski’s “Rule of Five” paper in the world of medicinal chemistry.

A beginning is a delicate time

Back in 2003, I started keeping a blog, because that’s what us happening young kids were doing then.  I still have all the files backed up somewhere, probably in a Google Drive folder, or on a defunct Mac Mini buried in my storage unit in Mission Bay in San Francisco.  In it, I wrote about life in Denmark, science, literature, and anything that caught my jackdaw eye on the internet.  It wasn’t brilliant, but it was mine.

For various reasons in about 2010 I stopped renewing the domain (daen.dk) and so it slipped from my grasp along with seven years of accumulated wisdom.  The world reeled from this loss, and then, somehow, managed to get a hold of itself and kept spinning.

It wasn’t so great a loss; I’d already turned to Facebook in around 2007 in order to dispense my joy and wisdom, as so many of us did in those halcyon days, through its happy blue balloon of a UI.

But lately, I find myself becoming more and more disillusioned with it as a medium to propagate anything other than cat photos or snarky posts about idiot politicians.  Something I enjoy is writing discursive essays on the state of various aspects of science, especially chemistry and genetic testing, and unfortunately Facebook is a less than perfect home for that kind of thing; it really doesn’t lend itself to long-form essays.

Which is why this new blog has been birthed, screaming and kicking, into the second month of the year.  Little does it know of the dreams and aspirations I have for it at its inception, the soaring and vicarious ambitions of the proud parent it will inspire along the way, or the bitter destination of disappointment and betrayal at which we will both inevitably arrive.

But I’m getting ahead of myself.

So rest, weary traveler, refresh yourself and your web browser, and dream of great things to come, for come they must!

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