Moon above
All the secrets I've told
When we're alone
Down here
I'm always lonely
When you're gone
— Down Here / Moon Above, Flunk (History of Everything Ever)
Why don't we send this music to space? What do you say?
Flunk has always had a special place in my heart. When I became involved in the Sanctuary Project — a kind of love letter to the Universe — I saw a way to say thank you to by favourite band.
So I invited them to come with me to somewhere distant and cold.
The Sanctuary Project is a Lunar vault for humanity, inspired by projects like the Golden Record and engraved on ten 10 cm sapphire discs. The discs include math, science, maps, poetry, art and a couple of jokes.
Oh, and a backup of our species. Push to reboot.
A couple of years ago, I reached out to Ulf Nygaard, the principal and founder of Flunk, and invited him to contribute a song to Sanctuary. Something that would sound great on the Moon.
“I'll make something perfect”, he said.
And then he did.
I sat down for drinks with Flunk in Oslo. We celebrated Hitchmas. Make it a double — we were going to go to the Moon.
“Ulf, why is this album called Chemistry and Math?” I asked about Flunk's latest album at the time. And perhaps one with the most unusual title.
I will never forget his answer.
“Sitting in a cafe, I saw two people crossing the street from opposite sides. As they passed each other in the middle, they recognized each other and started talking.”
“In the end, it's just chemistry and math.”
To me, this was the Mariana trench of deep romantic statments. I knew then Flunk was the perfect match for this project.
Ok, I knew thew before too.
On May 28th, Flunk released their new album History of Everything Every and Track 1 is Down Here / Moon Above.
While the original plan was for the song to make it to the Moon before its debut on Earth, this didn't quite happen. We're still working on the Moon angle.
Yes, I do science and make art and I love Flunk, but what does all this have to do with me.
Well, four of the Sanctuary discs contain the backup for humanity: fully sequenced genomes of a woman and man. The individuals were randomly and anonymously selected from our Healthy Aging Study lead by Dr. Angela Brooks-Wilson. The DNA was sequenced at Canada's Michael Smith Genome Sciences Center.
I designed and created the content for these discs, which not only include the genomes but also the proteome (gene protein sequences) and the chemical structures of associated metabolites. The genomes include about 10 million SNPs to represent all our variation (imagine me waving my hands around at this point). The SNPs are encoded inline with the sequence, so you do not actually know what the original sequenced genome was — at each position of variation you have a choice of bases.
The discs also contain art and snippes of culture (some pop and some not). It's basically a giant cosmic Easter egg.
Each disc is a 10 cm diameter sapphire wafer containing 3 billion 1-bit pixels.
They're thermodynamically inert and will last forever. Roughly speaking.
You can pixel-peep and browse each of the discs.
To me, these discs are a love poem to the Universe. Or a post card — I love post cards.
The four genome discs look like this.
You know you're done reading when you get to the end.
The first disc, which contains roughly the first half of the female genome, also contains instructions for decoding, along with a few of our learned lessons (Nuremberg Code and Declaration of Helsinki) that remind the reader not to experiment carelessly with the information.
Peeping a bit closer, these instructions take shape. the long black strip is a spectrogram encoding of Flunk's song. For a closeup of the decoding instructions for the discs, see the Instructions section.
Flunk's song is encoded using 128 mel 3-bit spectrogram. This takes 11,688 × 384 1-bit pixels on the discs. For details see the Sonogram section.
A 512 mel 1-bit encoding of the full History of Everything Ever album. Great for your wall or Moon patch.
Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry. – Richard Feynman
Following up on our Neural network primer column, this month we explore a different kind of network architecture: a convolutional network.
The convolutional network replaces the hidden layer of a fully connected network (FCN) with one or more filters (a kind of neuron that looks at the input within a narrow window).
Even through convolutional networks have far fewer neurons that an FCN, they can perform substantially better for certain kinds of problems, such as sequence motif detection.
Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Convolutional neural networks. Nature Methods 20:.
Derry, A., Krzywinski, M. & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.
Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.
Nature is often hidden, sometimes overcome, seldom extinguished. —Francis Bacon
In the first of a series of columns about neural networks, we introduce them with an intuitive approach that draws from our discussion about logistic regression.
Simple neural networks are just a chain of linear regressions. And, although neural network models can get very complicated, their essence can be understood in terms of relatively basic principles.
We show how neural network components (neurons) can be arranged in the network and discuss the ideas of hidden layers. Using a simple data set we show how even a 3-neuron neural network can already model relatively complicated data patterns.
Derry, A., Krzywinski, M & Altman, N. (2023) Points of significance: Neural network primer. Nature Methods 20:165–167.
Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.
Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.
Designed in collaboration with with Carlos Urzua.
Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).
Browse my gallery of cover designs.
My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes.
More details about the design.
Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9.
Browse my gallery of cover designs.
If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber
In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.
We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).
Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19:1513–1515.
My 5-dimensional animation sets the visual stage for Max Cooper's Ascent from the album Unspoken Words. I have previously collaborated with Max on telling a story about infinity for his Yearning for the Infinite album.
I provide a walkthrough the video, describe the animation system I created to generate the frames, and show you all the keyframes
The video recently premiered on YouTube.
Renders of the full scene are available as NFTs.