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And whatever I do will become forever what I've done.Wislawa Szymborskadon't rehearsemore quotes
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music + art
Equisitely detailed gigapixel 1-bit maps of the Moon (6,733 locations), Solar System (772,063 things) and the Northern and Southern skies (113,743,599 stars, 162,252 deepsky objects, 4,009 exoplanets).

There is no sound in space, but there is music (and genomes)

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The first 12 seconds of a 1-bit encoding of a 128 mel 3-bit spectrogram of Flunk's Down Here / Moon Above

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.

1 · Decoding instructions

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
THE INSTRUCTION MANUAL | A composite of the instructions for decoding the Sanctuary discs.

1.1 · EULA — E is for ethics

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 is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
HELLOW PEOPLE, READ THIS! | Getting started with the EULA. No funny business!

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.

1.2 · A galactic poem

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

2 · Instruction manual in 5 panels

Once we have the EULA out of the way, let's get into it.

2.1 · From LUCA to you and DNA

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.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Diving deep into the tree of life — from LUCA to our DNA.

2.2 · How the data are organized

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.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The encoding scheme. This better make sense.

2.3 · Amino acids and proteins

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.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
It's about the proteins. But you have to fold them.

2.4 · Exercise left for the reader

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”.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Decoding your first disc. A working example.

2.5 · What's on the discs — In numbers

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.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Checking your work. A tabulation of what is on the discs.

3 · Credits

The instruction panels end in a few "making of" scenes and a list of credits.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Credits and outtakes.

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?”

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The hand that sequenced this and a timestamp.

4 · Dedication to Michael Smith

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.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Dedication to Michael Smith.
Canada's Michael Smith Genome Sciences Centre (GSC) at BC Cancer is an international leader in genomics, proteomics and bioinformatics for precision medicine. By developing and deploying cutting-edge genome sequencing, computational and analytical technology, we are creating novel strategies to prevent and diagnose cancers and other diseases, uncovering new therapeutic targets and helping the world realize the social and economic benefits of genome science.
We are the Canadian node of the Earth Biogenome Project.

5 · Bibliography

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.

There is no sound in space, but there is music (and genomes) () -- science + art + data visualization / Martin Krzywinski / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A couple of papers that get you started on the topic of genomics.
news + thoughts

Nasa to send our human genome discs to the Moon

Sat 23-03-2024

We'd like to say a ‘cosmic hello’: mathematics, culture, palaeontology, art and science, and ... human genomes.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | A cosmic hello of art, science, and genomes. (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | Benoit Faiveley, founder of the Sanctuary project gives the Sanctuary disc a visual check at CEA LeQ Grenoble (image: Vincent Thomas). (details)
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
SANCTUARY PROJECT | Sanctuary team examines the Life disc at INRIA Paris Saclay (image: Benedict Redgrove) (details)

Comparing classifier performance with baselines

Sat 23-03-2024

All animals are equal, but some animals are more equal than others. —George Orwell

This month, we will illustrate the importance of establishing a baseline performance level.

Baselines are typically generated independently for each dataset using very simple models. Their role is to set the minimum level of acceptable performance and help with comparing relative improvements in performance of other models.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Comparing classifier performance with baselines. (read)

Unfortunately, baselines are often overlooked and, in the presence of a class imbalance5, must be established with care.

Megahed, F.M, Chen, Y-J., Jones-Farmer, A., Rigdon, S.E., Krzywinski, M. & Altman, N. (2024) Points of significance: Comparing classifier performance with baselines. Nat. Methods 20.

Happy 2024 π Day—
sunflowers ho!

Sat 09-03-2024

Celebrate π Day (March 14th) and dig into the digit garden. Let's grow something.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2024 π DAY | A garden of 1,000 digits of π. (details)

How Analyzing Cosmic Nothing Might Explain Everything

Thu 18-01-2024

Huge empty areas of the universe called voids could help solve the greatest mysteries in the cosmos.

My graphic accompanying How Analyzing Cosmic Nothing Might Explain Everything in the January 2024 issue of Scientific American depicts the entire Universe in a two-page spread — full of nothing.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
How Analyzing Cosmic Nothing Might Explain Everything. Text by Michael Lemonick (editor), art direction by Jen Christiansen (Senior Graphics Editor), source: SDSS

The graphic uses the latest data from SDSS 12 and is an update to my Superclusters and Voids poster.

Michael Lemonick (editor) explains on the graphic:

“Regions of relatively empty space called cosmic voids are everywhere in the universe, and scientists believe studying their size, shape and spread across the cosmos could help them understand dark matter, dark energy and other big mysteries.

To use voids in this way, astronomers must map these regions in detail—a project that is just beginning.

Shown here are voids discovered by the Sloan Digital Sky Survey (SDSS), along with a selection of 16 previously named voids. Scientists expect voids to be evenly distributed throughout space—the lack of voids in some regions on the globe simply reflects SDSS’s sky coverage.”

voids

Sofia Contarini, Alice Pisani, Nico Hamaus, Federico Marulli Lauro Moscardini & Marco Baldi (2023) Cosmological Constraints from the BOSS DR12 Void Size Function Astrophysical Journal 953:46.

Nico Hamaus, Alice Pisani, Jin-Ah Choi, Guilhem Lavaux, Benjamin D. Wandelt & Jochen Weller (2020) Journal of Cosmology and Astroparticle Physics 2020:023.

Sloan Digital Sky Survey Data Release 12

constellation figures

Alan MacRobert (Sky & Telescope), Paulina Rowicka/Martin Krzywinski (revisions & Microscopium)

stars

Hoffleit & Warren Jr. (1991) The Bright Star Catalog, 5th Revised Edition (Preliminary Version).

cosmology

H0 = 67.4 km/(Mpc·s), Ωm = 0.315, Ωv = 0.685. Planck collaboration Planck 2018 results. VI. Cosmological parameters (2018).

Error in predictor variables

Tue 02-01-2024

It is the mark of an educated mind to rest satisfied with the degree of precision that the nature of the subject admits and not to seek exactness where only an approximation is possible. —Aristotle

In regression, the predictors are (typically) assumed to have known values that are measured without error.

Practically, however, predictors are often measured with error. This has a profound (but predictable) effect on the estimates of relationships among variables – the so-called “error in variables” problem.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Error in predictor variables. (read)

Error in measuring the predictors is often ignored. In this column, we discuss when ignoring this error is harmless and when it can lead to large bias that can leads us to miss important effects.

Altman, N. & Krzywinski, M. (2024) Points of significance: Error in predictor variables. Nat. Methods 20.

Background reading

Altman, N. & Krzywinski, M. (2015) Points of significance: Simple linear regression. Nat. Methods 12:999–1000.

Lever, J., Krzywinski, M. & Altman, N. (2016) Points of significance: Logistic regression. Nat. Methods 13:541–542 (2016).

Das, K., Krzywinski, M. & Altman, N. (2019) Points of significance: Quantile regression. Nat. Methods 16:451–452.

Convolutional neural networks

Tue 02-01-2024

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).

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Convolutional neural networks. (read)

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 20:1269–1270.

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.

Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA
Google whack “vicissitudinal corporealization”
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