There is no sound in space, but there is music
contents
The discs contain the full genome of a female and male as well as the human proteome and metabolome.
The genome sequence is organized into panels of 203 × 203 pixels. Each panel contains 202 × 202 = 40,804 data pixels. The last row and column are dedicated to error correction — registering whether the sum of a row or column pixels is even.
Each disc contains about about 70,000 such panels comprising about 2,800,000,000 pixels. For every 1,024 panels, there is an error check panel that works like the row/column error check except that it sums across panels.
Each base is encoded by two pixels so each panel stores 20,402 bases. Each disc therefore stores about 1.4 Gb of sequence. This capacity is just enough to store the fully sequenced haploid genome of an individual on two discs.
The proteome is stored in smaller panels of size `n` × 32 where `n=2-32`. These panels are placed near the edge of the disc to make full use of the space on the disc.
The proteome ends close to the start of the last disc. From this point on, the small panels are used to store the chemical structures of compounds that participate in metabolic reactions.
Each compound is a jigsaw puzzle — its structure is stored across one or more panels and it's up to you to piece the panels together. Hint: the first panel of a structure has its pixels inverted.
Each disc also includes a jigsaw puzzle — four in total.
You put it together. And by you I mean they. And by they I mean (possibly) aliens.
If you like these puzzles, see my 1-bit 10 gigapixel space maps.
The first female disc has a moon map puzzle. The “She looks like the Moon” is a reference to Like the Moon by Future Islands.
The second female disc has the solar system. Not everything in it but closeish to it.
The north celestial hemisphere is the puzzle on the first male disc. Hence, ‘No Man's Sky’. Except that there is a man — on the disc. But it's not his sky. This is what I meant.
‘My God, it's also full of stars.’ Keep coruscatling, little buddies!
The first disc also contains a collection of 124 artworks by children undergoing treatment in Paris hospitals.
This was organized by Jean-Philippe Uzan who is part of the Les p'tits cueilleurs d'étoiles program (The Little Star Gatherers), designed to bring space to hospitalized children.
You can browse the full gallery.
There are many other curious things to find on the first disc. Here are some of them.
Convolutional neural networks
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:.
Background reading
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.
Neural network primer
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.
Background reading
Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nature Methods 13:541–542.
Cell Genomics cover
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.
Science Advances cover
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.
Regression modeling of time-to-event data with censoring
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.
Music video for Max Cooper's Ascent
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.