"I wish I were Nigella Lawson"

I say to her:

"Suppose you said, 'I wish I were Nigella Lawson,' .. given as how you like her.

So imagine your genome hanging in the air and next to it Nigella's.

Sequencing projects find about one SNP per 1000 bases. That's the basis for the claim that people are 99.9% genetically similar. The human genome is about 3 Gbp long. This suggests about 3 million SNPs are different among two random people.

So imagine molecular scissors tweaking your genome: three million base pair edits until we've made you into Nigella, ta-da!

But wait! We already have a Nigella. In every important sense your wish has already come true!"

--- pause ---

"I thought for a moment you were going to say something sensible."

DNA.Land

As I have my partially-sequenced genome over at 23andMe, I decided to do my bit for genetic research by signing up with DNA.Land.

Purpose

"DNA.Land is a place where you can learn more about your genome while enabling scientists like us to make new discoveries for the benefit of humanity. The website is not-for-profit and run by the Erlich and Pickrell labs affiliated with Columbia University and the New York Genome Center.

"The purpose of DNA.Land is to enable you to learn more about your DNA and allow you the autonomy to share your data to facilitate important scientific research at the forefront of genome sciences and medicine. Our goal is to help members interpret their data and connect potential participants with research studies.

Procedures

"After you provide consent, your participation would consist of creating your personal profile and securely uploading your genetic data to DNA.Land. We will use the most cutting edge genetic tools to analyze your data and return your results regarding ancestry, relatives, and different traits.

"As we want to learn about the genetic basis of different traits, we will ask you to fill out surveys relating to your (or your family’s) ancestry and health. You will also have the option to automatically contribute data from your social media profiles for new types of analysis, so we can learn about traits that are dynamic and more difficult to measure, such as social preferences.

"Your profile will also display a badge that summarizes your various contributions to DNA.Land. You can tweet this badge, share it on Facebook, or sew it on your old scout uniform.

"There are no costs associated with taking part in DNA.Land and you will not be compensated for participating."

Where is the value-add over, say, the 23andMe health and ancestry reports? DNA.Land 'impute' missing parts of your genome based on "whole genome sequencing data used to create a dictionary of genomic 'text' (known as haplotypes)."

So how does this help?

"Uploaded genotype files (e.g. from 23andMe) contain between 500,000 to 1 million SNPs. DNA.Land's imputation pipeline imputes (i.e. infers the value of) an additional 38 million SNPs."

I guess this exploits linkage disequilibrium.

After many hours of crunching, DNA.Land will deliver an imputed VCF file (about half a Gigabyte). They attempt to explain how to interpret this ("Understanding VCF values") - but it will plainly take more work on my part to figure it out. The raw detail file - in all its immensity - seems pretty opaque; probably best to run the whole thing through Promethease.

Here's what SNPedia says about DNA.Land with reference to Promethease.

And here's how to run the imputed results through Promethease. Haven't tried it as the file isn't yet available, I think it's just use the "Upload Raw data" button.

Costs $10 for the enhanced ('imputed') report.

So I'm currently waiting for DNA.Land's computers to finish crunching my 23andMe raw data file.

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Update: (Tuesday 3.22 pm): Promethease currently uploading 417 MB of dnl13394_inl.imputed.vcf via ADSL. A long wait ahead.

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Update: (Tuesday 7.29 pm): OK, so all done.

I have the Promethease report downloaded, all 8 MB of it. Time enough to browse it tomorrow.

I rather wish that Promethease had told me it doesn't accept .bcf files (the binary version of .vcf) before I uploaded half a Gigabyte's worth - how hard could that be, to check a file extension?

It did, however, take .vcf so it all worked in the end.

The implacable state; Autonomous AI; 23andMe as a family investment

I was reduced to helpless, incandescent fury this morning by the unexpected arrival of a speeding ticket. I had been caught on camera on the way to my mother's funeral on Monday, Dec 21st 2015. I have applied for the driving awareness course option and will let you know in due course how it went, if accepted.

I visualise the Speed Enforcement Unit putting this together, chuckling as they did so.

Turns out I was doing 35 mph in a 30 mph section of the A-road at Westbury-on-Trym, Bristol. Once my head-banging, visceral anger had subsided (a trip to the gym helped considerably) I found the list above of more or less lame excuses (none of which work) quite amusing.

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Robin Hanson has an interesting piece about a newish book, 'Our Robots, Ourselves: Robotics and the Myths of Autonomy' by Prof. David Mindell at MIT. The book argues:

"If robotics in extreme environments are any guide, Mindell says, self-driving cars should not be fully self-driving. That idea, he notes, is belied by decades of examples involving spacecraft, underwater exploration, air travel, and more. In each of those spheres, fully automated vehicles have frequently been promised, yet the most state-of-the-art products still have a driver or pilot somewhere in the network. This is one reason Mindell thinks cars are not on the road to complete automation.

“That’s just proven to be a loser of an approach in a lot of other domains,” Mindell says. “I’m not arguing this from first principles. There are 40 years’ worth of examples.”

As someone who is interested in AI and its impact on the automation of everyday tasks, I promptly bought the book (Kindle) and will let you know how compelling I think his arguments are. After my speeding ticket I am thinking wistfully - and defensively - about Google cars. How does anyone drive on a regular basis in the UK without collecting 12 points in short order and losing their licence?

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In August 2014 I persuaded my mother to donate a spit sample to 23andMe. Eventually I was able to show her the report plus the much more detailed information from Promethease. My mother had no technical interests and in particular no background in genetics. Nevertheless she read all the material in the folder with close attention for half an hour and then took possession of it, refusing to allow its contents to be shared with anyone else, even close family.

I think there was a little bit of magical thinking here, as the information was in no way earth-shattering. However, the reason I signed her up was in anticipation of a future where 23andMe provide a full genome description and we actually know what it means. It's a family history gift to future generations. I might have mentioned to her that we could clone her from this data, bring her back memoryless, but I doubt she took it on board!

My father unfortunately died in 2009, before 23andMe got into business. I have some of his personal effects in storage anticipating future DNA profiling ... .

On an adjacent topic, it's interesting to see the latest genomic news on the ancestry of the Irish. Razib Khan has an in-depth discussion.