There is no sound in space, but there is music
contents
Here I show the decoding instructions that appear on the first disc. These took forever to make, were a lot of fun to make, and might require a full alien civilization to decode.
The instructions begin with an important announcement "Hello people read this!" followed by Huffman-encoded Nuremberg Code and Declaration of Helsinki. I explain how to decode the Huffman encoding.
There's lots of art and graphical notions on the discs. Here you see an amoeba and fairyfly — drawn at physical scale on the discs. Each pixel on the disc is 1.4 microns, so 100 microns is about 70 pixels. The images shown here are magnified for easier reading.
You also see a short space poem created out of an alphabetically ordered triplets of classification terms from the Atlas of Peculiar Galaxies. “To unclassified wind!”
absorption adjacent amorphous and appearance arm associated attraction brightness chains close clumps companions concentric connected counter-tail detached diffuse disturbed double effects ejected ellipticals emanating filaments fission fragments from galaxies groups heavy high infall integral interacting interior irregular irregularities jets large long loops low material miscellaneous multiple narrow nearby nuclei objects of one one-armed or perturbing pōwehi repelling resolution rings segments sign small spiral split surface three-armed to unclassified wind
Once we have the EULA out of the way, let's get into it.
The first instruction panel begins with a piece of Alan Watts' It Starts Now, dedicated to our last universal common ancestor (LUCA). “You are this universe...”
We see the tree of life (I apologize for the millions of sparks of life that aren't listed) and you're taken along the branching all the way to us, into our cells and into the bases of our DNA that are on the discs. It's quite a trip.
The next panel shows how the data is organized on the discs and how it's encoded. All amidst a story of dinosaur struggle.
The pixel stream on the discs contain metadata codes (it was fun to find the shorted codes that didn't appear in the sequence). For example, SNPs of each class (e.g. A/T) are indicated by unique sequence of bits.
The genome is just a kind of recipe book for proteins. So the next panel explains how these are made up of amino acids. I mention that they fold but leave the details of the folding as an exercise to the audience. We can't be expected to figure out everything ourselves.
Next, to practise what you've learned, there is a little practical example of decoding a baby disc. Also the final panel of the dinosaur story appears here — many things are out of order on the discs and the reader is encouraged to piece them together. Yes, “death is very very long”.
Once you've decoded the discs, you can check your work against this table. The number of bits, bases and SNPs on each disc are shown.
The instruction panels end in a few "making of" scenes and a list of credits.
I took a photo of Steve Chand holding the flowcell before he loaded the sequencer. The map of the solar system answers the question “When did he load the sequencer?”
Our Center was founded by Michael Smith. The discs include a short dedication and a nostalgic photo of his office that I took shortly after he died.
We wouldn't be here without the seminal papers of Franklin and of Watson and Crick. Ok we would be here without them but we wouldn't know ourselves as well.
The Nature mansucripts are lovingly typeset here.
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.