Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - contact me Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert CurveMartin Krzywinski / Canada's Michael Smith Genome Sciences Centre / mkweb.bcgsc.ca - Pi Day 2020 - Piku
Trance opera—Spente le Stellebe dramaticmore quotes

b: 2


Scientific graphical abstracts — design guidelines


data visualization + art

If you like space, you'll love my 2017 Pi Day art which imagines the digits as a star catalogue. Meet the Quagga and Aurochs—the Constellations in this sky are extinct animals and plants.

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from an undefined
place,
undefined
create (a place)
an account
of us
— Viorica Hrincu

Sometimes when you stare at the void, the void sends you a poem.

Universe—Superclusters and Voids

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The Universe — Superclustesr and Voids. The two supergalactic hemispheres showing Abell clusters (blue), superclusters (magenta) and voids (black) within a distance of 6,000 million light-years from the Milky Way.

The average density of the universe is about `10 \times 10^{-30} \text{ g/cm}^3` or about 6 protons per cubic meter. This should put some perspective in what we mean when we speak about voids as "underdense regions".

the ultimate rabbit hole

It started as a two-hour project: generate a small map of superclusters for the space disc of the Sanctuary project.

I was going to simply trace this map of superclusters within 2 billion light-years and be done with it. But nobody strapped me to the mast of my boat—the Siren call of the rabbit hole proved too appealing.

Why settle for a copy of someone else's map to within (only) 2 billion light-years when you can trawl the VizieR astronomical databases and get thousands of objects out to 6 billion light-years. You can then swear and fret about how to interpret these data, read about celestial coordinate systems, implement your own primitive 3D engine and write stories about the farthest reaches.

vast somethingness and nothingness

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The largest map there is. Shown are Abell clusters, superclusters and voids in the Universe within a distance of 6,000 million light-years from earth. If you look close enough, you can also find the quasar J1342+0928, which is 13,000 million light-years away and is currently the furthest observed quasar in the Universe. (zoom)

This map of the Universe shows 3,751 Abell galaxy clusters (blue), 1,024 galaxy superclusters (magenta) and 2,042 voids (black). Objects are drawn using the supergalactic coordinate system within a sphere that is 12,000 million light-years in diameter.

Around the poster are various stories about constellations, stars, sky mythology, coordinate systems and, of course, voids.

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Progressive zooms of a region in the North Supergalactic Hemisphere in the neighbourhood of the Boötes void. In the foreground, projected on the supergalactic sphere, is the constellation Ursa Minor. (zoom)

poem on the poster

This poster is an artistic collaboration with Viorica Hrincu, a brilliantly talented poet.

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Poem by Viorica Hrincu. (zoom)

stories on the poster

the constellations and the equators

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 88 constellations are projected onto the supergalactic sphere. Also shown are the galactic and celestial equators. (zoom)

The 88 constellations are projected onto the supergalactic sphere and labeled by their abbreviations. Those falling on the back of the sphere drawn with fainter lines.

The Celestial North Pole is very close to Polaris in Ursa Minor. It is connected to the center of the sphere by a dotted white line, which continues to Celestial South Pole in the constellation Octantis.

Also shown are the galactic and celestial galactic equators, which form the basis of other coordinate systems.

The lines of supergalactic longitude and latitude in this map are scaled to expand the scale at smaller supergalatic latitudes. The scale is also compressed for longitudes near the galatic equator, where observations are obscured by the stars in the Milky Way.

See my IAU Constellation Resources for more details.

oh my god, it's full of stars

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The stars of the Yale Bright Star Catalogue are projected onto the supergalactic sphere. (zoom)

The 9,096 stars in the Yale Catalogue of Bright Stars. Each star in the catalogue is assigned a unique HR designation. The HR prefix is named after the Harvard Revised Photometry Catalogue, which is the Yale’s catalogue predecessor.

The briggest star in the catalogue is Sirius (HR 2491), also known as the Dog Star. The dimmest star in the catalogue (HR 1894) is found very close to Sirius, in the constellation Orion.

Both of these constellations are found at the bottom of the supergalactic sphere.

HUNTTER’S BEST FRIENDS

After Orion was killed from the bite of a scorpion, Zeus placed him in the sky and arranged the sky to keep Orion safe. Now, when Scorpio rises in the east, Orion sets.

Orion is accompanied by his loyal hunting dogs, Canis Major and Canis Minor, who protect the hunter from danger—Earthly and Heavenly. The larger dog companion lights the way with Sirius, the sky’s brighest star.

THE TRAPEZIUM

A cluster of stars at the heart of the Orion nebula in the constellation Orion.

The Trapezium was discovered by Galileo and contains θ1 Ori B, the dimmest star in the Yale Catalogue of Bright stars. This is a variable star, which drops in brightness from magnitude 7.96 to about 8.65 for 8–9 hours every 6.5 days.

coordinate system—finding your way

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The relationship between supergalactic, galactic and equatorial celestial coordinate systems. (zoom)

Objects in the sky can be referenced using various coordinate systems. The supergalactic system, used in this map, has its equator aligned to the planar-like distribution of the local group of galaxies near the Milky Way. This system is useful for very distant objects.

The galactic system is aligned to the plane of the Milky Way. Its North Pole lies directly above the Milky Way. The plane of the MIlky Way is almost perpendicular to the plane of the supergalactic system. This places most of the stars of the Milky Way lie close to the meridian (0°) and antimeridian (180°) of supergalactic longitude.

The equatorial system is aligned to the equator of the Earth and uses the familiar right ascension (longitude) and declination (latitude) position variables. The celestial North Pole is very close to Polaris in Ursa Major and the South Pole is close to the star σ Octantis, also known as Polaris Australis.

Celestial coordinates are associated with an epoch for which the coordinates are most accurate. Most modern coordinates are specified to J2000, the 2000th Julian year. Converting between epochs is required to correct for precession or to make use of data sets that reference a different epoch. For example, the boundaries of the constellations are defined relative to the year 1875.

The ecliptic system, not shown here, has its equator as the Earth’s orbit in the Solar System. It uses ecliptic longitude β and latitude λ as its variables and is useful for specifying positions within the Solar System.

reading the map

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Objects are drawn within the supergalactic sphere and projected onto the supergalatic equator. (zoom)

Objects on the map are drawn using the supergalactic coordinate system. Their relative position can be resolved using the vertical line that projects their position onto the supergalactic equator. For objects of the same type in the same neighbourhood, only one vertical line is drawn. The radius of the sphere is 6 billion light-years.

Shown here are three superclusters (403, 409 and 411) in the constellation Boötes along with the 25 Abell clusters that they comprise.

For example, supercluster 403 has a redshift of z = 0.041, which places it at a distance of about 550 Mly. Its position in the sky in equatorial coordinates is right ascension 13h 49m and declination +32° 40’ 12.4”. Expressed in the supergalactic coordinate system, this position is supergalactic longitude (SGL) of 86.8° and latitude (SGB) of 19.6°.

Further Than You Think

Distances on the map are expressed as light-travel distances—how long it has taken light from an object to reach us today. However, because of the expansion of the Universe, the actual distance to an object is larger—this is known as the comoving distance and accounts for the fact that during the time that the light took to reach us, space has expanded.

For example, the most distant object we have observed is the galaxy GN-Z11, from which light took 13.3 billion years to reach us. This galaxy was formed only about 400 million years after the Big Bang. Since then, space has expanded and today this galaxy is 32.2 Gly away.

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The expansion of space can make calculating distances complicated. Two distances are commonly referenced: light-travel distance and comoving distance. (zoom)

the cosmic yardstick

One of the consequences of the expanding Universe is the cosmological redshift, which can be used as a measure of distance. Because light is travelling in an expanding space, by the time it reaches us its wavelength has increased. For example, the galaxy The galaxy GN-Z11 has a redshift of `z` = 11.09.

The mathematical relationship between the redshift and distances depends on several cosmological constants, such as the Hubble constant, `H_0` = 68.6 kms/(s·Mpc), and matter density, `\Omega_M = 0.286`. Using these values, we can calculate the age of the universe (light-travel distance for an object with infinite redshift) as 13.7 billion years and its observable radius (the comoving distance of this object) as 46.4 billion light-years.

The Long Goodbye

The expansion of space imposes other consequences. In the far-distant future (`10^{11}` years), we will no longer be able to observe many of the distant objects that we see today—a grim prospect for future astronomers. And, as light from distant objects fades beyond detection, their image will be frozen at a fixed age.

Nothing out of nothing—voids and supervoids

Cosmic voids are part of the large-scale structure of the Universe. They are vast spaces that contain very few or no galaxies. Voids typically have a diameter of 35 to 350 Mly—those that are particularly large and lack rich superclusters are called supervoids. They were first discovered in 1978 in a tephen Gregory and Laird A. Thompson at the Kitt Peak National Observatory.

Voids have less than one tenth of the average matter density found in the Universe. They are thought to have been caused by oscillations of matter during the Big Bang—collapses of mass followed by implosions. These oscillations gave rise to small differences in the distribution of mass in the early Universe that grew over time. Dense areas collapsed more rapidly under gravity and created the foam-like structure of galaxy filaments and voids we observe today.

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The North Supergalactic Hemisphere is home to the Boötes void, the Northern Local Supervoid and the Giant Void, among others. (zoom)

The Boötes Void

The Boötes Void is named after the constellation in which it is found and is one of the largest-known voids in the Universe. It is about 700 million light-years away and 330 million light-years in diameter. While there should be about 2,000 galaxies in this region, so far only 60 have been found.

The Northern Local Supervoid

The Northern Local Supervoid is the closest supervoid to us. Its proximity has allowed detailed observation, revealing a network of faint galaxy systems that divide it into 103 smaller voids, ranging in size from 10 to 130 Mly and in distance from 55 to 390 Mly. These smaller voids lie between 12h 12m 12s and 17h 21m 36s) right ascension and between +5° 48’ and +66° 24’ declination.

The Giant Void

The Giant Void is in the constellation Canes Venatici. It is the second largest confirmed void to date. Although this void is vastly empty, it contains 17 galaxy clusters, concentrated in a region 160 Mly in diameter.

River in the sky—Eridanus supervoid

Eridanus is one of the 48 constellations listed by the 2nd century astronomer Ptolemy. It is represented as a river and is the sixth largest of the 88 modern constellations. The same name was later taken as a Latin name for the real Po River in Northern Italy as well as the name of a river in Athens.

This constellation contains a curious object.

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The river constellation Eridanus and its unusual object: the Eridanus supervoid, also known as the CMBR Cold Spot. (zoom)

Great, not Giant, Void

The Eridanus Supervoid is also know as the Great Void, not to be confused with the Giant Void in Canes Venatici in the Northern hemisphere.

This supervoid is a an extremely large region of the Universe, roughly 500–1,000 million light-years across and 6–10 billion light-years away.

The Eridanus Supervoid hasn’t been observed directly as a void—it is postulated as an explanation for a region of space in which the cosmic microwave background radiation (CMBR) is particularly weak, known as the CMBR Cold Spot.

The Cold Spot is 70 μK colder than the average CMB temperature of 2.7 K. In some areas, the cold spot is 140 μK colder—roughly 8 times the root mean square variation of the CMBR. If the Cold Spot is indeed a supervoid, it would be one of the largest structures ever observed.

far out—J1342+0928

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The quasar J1342+0928 is thus far the most distant object ever observed. (zoom)

The quasar J1342+0928 is the most distant quasar, far outside the map’s sphere. Currently, the furthest observed object is the galaxy GN-Z11, which is 13.4 billion light-years away.

Poster Legend

Universe - Superclusters and Voids / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The Universe: Superclusters and voids. (zoom)

The map shows 3,751 Abell galaxy clusters, 1,024 galaxy superclusters and 2,042 voids. Supercluster and void circles are scaled to their estimated size. Abell clusters are scaled based on the number of galaxies in the cluster. Most objects are named after the constellation in which they are located. The sphere is based on the supergalactic coordinate system and has a diameter of 12 billion light-travel years. The supergalactic equator is aligned to the planar-like distribution of galaxies in the Milky Way. The vertical distance of an object from the equator is a function of the latitude and distance of the object. For readability, the latitude and longitude are scaled to improve visual separation of objects and the sphere is split into the Northern and Southern Supergalactic Hemispheres.

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news + thoughts

Graphical Abstract Design Guidelines

Fri 13-11-2020

Clear, concise, legible and compelling.

Making a scientific graphical abstract? Refer to my practical design guidelines and redesign examples to improve organization, design and clarity of your graphical abstracts.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Graphical Abstract Design Guidelines — Clear, concise, legible and compelling.

"This data might give you a migrane"

Tue 06-10-2020

An in-depth look at my process of reacting to a bad figure — how I design a poster and tell data stories.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A poster of high BMI and obesity prevalence for 185 countries.

He said, he said — a word analysis of the 2020 Presidential Debates

Thu 01-10-2020

Building on the method I used to analyze the 2008, 2012 and 2016 U.S. Presidential and Vice Presidential debates, I explore word usagein the 2020 Debates between Donald Trump and Joe Biden.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Analysis of word usage by parts of speech for Trump and Biden reveals insight into each candidate.

Points of Significance celebrates 50th column

Mon 24-08-2020

We are celebrating the publication of our 50th column!

To all our coauthors — thank you and see you in the next column!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance: Celebrating 50 columns of clear explanations of statistics. (read)

Uncertainty and the management of epidemics

Mon 24-08-2020

When modelling epidemics, some uncertainties matter more than others.

Public health policy is always hampered by uncertainty. During a novel outbreak, nearly everything will be uncertain: the mode of transmission, the duration and population variability of latency, infection and protective immunity and, critically, whether the outbreak will fade out or turn into a major epidemic.

The uncertainty may be structural (which model?), parametric (what is `R_0`?), and/or operational (how well do masks work?).

This month, we continue our exploration of epidemiological models and look at how uncertainty affects forecasts of disease dynamics and optimization of intervention strategies.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (read)

We show how the impact of the uncertainty on any choice in strategy can be expressed using the Expected Value of Perfect Information (EVPI), which is the potential improvement in outcomes that could be obtained if the uncertainty is resolved before making a decision on the intervention strategy. In other words, by how much could we potentially increase effectiveness of our choice (e.g. lowering total disease burden) if we knew which model best reflects reality?

This column has an interactive supplemental component (download code) that allows you to explore the impact of uncertainty in `R_0` and immunity duration on timing and size of epidemic waves and the total burden of the outbreak and calculate EVPI for various outbreak models and scenarios.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Uncertainty and the management of epidemics. (Interactive supplemental materials)

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Uncertainty and the management of epidemics. Nature Methods 17.

Background reading

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: Modeling infectious epidemics. Nature Methods 17:455–456.

Bjørnstad, O.N., Shea, K., Krzywinski, M. & Altman, N. (2020) Points of significance: The SEIRS model for infectious disease dynamics. Nature Methods 17:557–558.

Cover of Nature Genetics August 2020

Mon 03-08-2020

Our design on the cover of Nature Genetics's August 2020 issue is “Dichotomy of Chromatin in Color” . Thanks to Dr. Andy Mungall for suggesting this terrific title.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Dichotomy of Chromatin in Color. Nature Genetics, August 2020 issue. (read more)

The cover design accompanies our report in the issue Gagliardi, A., Porter, V.L., Zong, Z. et al. (2020) Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes. Nature Genetics 52:800–810.