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Trance opera—Spente le Stellebe dramaticmore quotes

a: 2


In Silico Flurries: Computing a world of snow. Scientific American. 23 December 2017


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.

null
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".

expressing distances in the universe

All distances on the poster are expressed in terms of the light travel distance.

light-travel and comoving distance

Distances in the universe can be expressed as either the light-travel distance or the comoving distance to the object. The first tells us how long light took to travel from the object to us.

For example, the furthest object observed is the galaxy GN-Z11 and its light-travel distance is 13 billion light-years (Gly).

But because space has expanded during the time the light from GN-Z11 has been travelling to us, the galaxy is now actually much further away. This is measured by its comoving distance which accounts for space expansion, which is 29.3 Gly for GN-Z11.

The redshift, `z`, is commonly used to specify distance, since it's a quantity that can be observed. For GN-Z11, `z = 11.09`.

calculating distances

To calculate these distances, the redshift `z` is used along with a few cosmological parameters.

The Hubble parameter, `H(z)`, is the function used for these calculations. It can be derived from the Friedmann equation. $$ H(z) = H_0 \sqrt { \Omega_r({1+z})^4 + \Omega_m({1+z})^3 + \Omega_k({1+z})^2 + \Omega_\Lambda } $$

The values of the parameters in `H(z)` are being continually refined and the values of some depend on various assumptions. I use the Hubble constant `H_0 = 69.6 \text{ km/s/Mpc}`, mass density of relativistic particles `\Omega_r = 8.6 \times 10^{-5}`, mass density `\Omega_m = 0.286`, curvature `\Omega_k = 0` and dark energy fraction `\Omega_\Lambda = 1 - \Omega_r - \Omega_m - \Omega_k = 0.713914`.

Bennett, C.L. et al The 1% Concordance Hubble Constant Astrophysical Journal 794 (2014)

Now given a redshift, `z` the light-travel distance is $$ d_T(z) = c \int_0^z \frac{dx}{({1+x})E(x)} $$

The age of the universe can be computed from this expression. The edge of the universe has an infinite redshift so w can calculate it using `\lim_{z \rightarrow \infty} d_T(z)`.

The comoving distance to the object with redshift `z` is $$ d_C(z) = c \int_0^z \frac{dx}{E(x)} $$

It's convenient to express the above integrals by making a variable substitution. Using the scale factor `a = 1/(1+z)`, $$E(a) = H_0 \sqrt { \frac{\Omega_r}{a^2} + \frac{\Omega_m}{a} + \Omega_k + a^4\Omega_\Lambda } $$

The light-travel distance is $$D_T(z) = c \int_a^1 \frac{dx}{E(x)}$$

The comoving distance is $$D_C(z) = c \int_a^1 \frac{dx}{xE(x)}$$

The light-travel distance to the edge of the universe is $$D_{T_U}(z) = c \int_0^1 \frac{dx}{E(x)}$$

and the light-travel distance from the edge of the universe to the object as we're observing it now is $$D_{T_0}(z) = c \int_0^a \frac{dx}{E(x)}$$

which can be interpreted as the age of the object when it emitted the light that we're seeing now.

The proper size of the universe is the comoving distance to its edge, $$D_{C_U}(z) = c \int_0^1 \frac{dx}{xE(x)}$$

distance calculator

Below you can You can download the full script.

### Cosmological distance calculator
### Martin Krzywinski, 2018
#
# The full script supports command-line parameters
# http://mkweb.bcgsc.ca/universe-voids-and-superclusters/cosmology_distance.py

z  = 1                     # redshift 
a  = 1/(1+z)               # scale factor
Wm = 0.286                 # mass density
Wr = 8.59798189985467e-05  # relativistic mass
Wk = 0                     # curvature
WV = 1 - Wm - Wr - Wk      # dark matter fraction
n  = 10000                 # integration steps

# Hubble parameter, as function of a = 1/(1+z)
def Ea(a,Wr,Wm,Wk,WV):
    return(math.sqrt(Wr/a**2 + Wm/a + Wk + WV*a**2))

H0   = 69.6            # Hubble constant
c    = 299792.458      # speed of light, km/s
pc   = 3.26156         # parsec to light-year conversion
mult = (c/H0)*pc/1e3   # integrals are in units of c/H0, converts to Gy or Gly
sum_comoving = 0
sum_light    = 0
sum_univage  = 0
sum_univsize = 0

for i in range(n):
    f   = (i+0.5)/n
    x   = a + (1-a) * f # a .. 1
    xx  = f             # 0 .. 1
    ex  = Ea(x,args.Wr,args.Wm,args.Wk,args.WV)
    exx = Ea(xx,args.Wr,args.Wm,args.Wk,args.WV)
    sum_comoving += (1-a)/(x*ex)
    sum_light    += (1-a)/(  ex)
    sum_univsize += 1/(xx*exx)
    sum_univage  += 1/(   exx)

results = [mult*i for i in [sum_univage,sum_univsize,sum_univage-sum_light, \
                            sum_light,sum_comoving]]
print("z {:.2f} U {:f} Gy {:f} Gly T0 {:f} Gy T {:f} Gly C {:f} Gly". \
      format(args.z,*results))

Use the script to generate distances for a given redshift, `z`. For example,

# For galaxy GN-Z11, furtest object ever observed
./cosmology_distance.py -z 11.09
z 11.09 U 13.720 Gy 46.441 Gly T0 0.414 Gy T 13.306 Gly C 32.216 Gly

The galaxy GN-Z11 has a light-travel distance of 13.3 Gly and a comoving distance of 32.2 Gly. We're seeing it now as it was only 0.4 Gy after the beginning of the universe, which is 13.7 Gy old and the distance to its edge is 46.4 Gly.

# For quasar J1342+0928, furthest quasar ever observed
./cosmology_distance.py -z 7.54
z 7.54 U 13.720 Gy 46.441 Gly T0 0.699 Gy T 13.021 Gly C 29.355 Gly

The values for U (age and size of universe), will always be the same for a given set of cosmological parameters for any value of `z`. I include them in the output of the script for convenience.

These values match those generated by Ned's online cosmological calculator for a flat universe.

VIEW ALL

news + thoughts

Molecular Case Studies Cover

Fri 06-07-2018

The theme of the April issue of Molecular Case Studies is precision oncogenomics. We have three papers in the issue based on work done in our Personalized Oncogenomics Program (POG).

The covers of Molecular Case Studies typically show microscopy images, with some shown in a more abstract fashion. There's also the occasional Circos plot.

I've previously taken a more fine-art approach to cover design, such for those of Nature, Genome Research and Trends in Genetics. I've used microscopy images to create a cover for PNAS—the one that made biology look like astrophysics—and thought that this is kind of material I'd start with for the MCS cover.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Cover design for Apr 2018 issue of Molecular Case Studies. (details)

Happy 2018 `\tau` Day—Art for everyone

Wed 27-06-2018
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
You know what day it is. (details)

Universe Superclusters and Voids

Mon 25-06-2018

A map of the nearby superclusters and voids in the Unvierse.

By "nearby" I mean within 6,000 million light-years.

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

Datavis for your feet—the 178.75 lb socks

Sat 23-06-2018

In the past, I've been tangentially involved in fashion design. I've also been more directly involved in fashion photography.

It was now time to design my first ... pair of socks.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Some datavis for your feet: the 178.75 lb socks. (get some)

In collaboration with Flux Socks, the design features the colors and relative thicknesses of Rogue olympic weightlifting plates. The first four plates in the stack are the 55, 45, 35, and 25 competition plates. The top 4 plates are the 10, 5, 2.5 and 1.25 lb change plates.

The perceived weight of each sock is 178.75 lb and 357.5 lb for the pair.

The actual weight is much less.

Genes Behind Psychiatric Disorders

Sun 24-06-2018

Find patterns behind gene expression and disease.

Expression, correlation and network module membership of 11,000+ genes and 5 psychiatric disorders in about 6" x 7" on a single page.

Design tip: Stay calm.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An analysis of dust reveals how the presence of men, women, dogs and cats affects the variety of bacteria in a household. Appears on Graphic Science page in December 2015 issue of Scientific American.

More of my American Scientific Graphic Science designs

Gandal M.J. et al. Shared Molecular Neuropathology Across Major Psychiatric Disorders Parallels Polygenic Overlap Science 359 693–697 (2018)

Curse(s) of dimensionality

Tue 05-06-2018
There is such a thing as too much of a good thing.

We discuss the many ways in which analysis can be confounded when data has a large number of dimensions (variables). Collectively, these are called the "curses of dimensionality".

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Curse(s) of dimensionality. (read)

Some of these are unintuitive, such as the fact that the volume of the hypersphere increases and then shrinks beyond about 7 dimensions, while the volume of the hypercube always increases. This means that high-dimensional space is "mostly corners" and the distance between points increases greatly with dimension. This has consequences on correlation and classification.

Altman, N. & Krzywinski, M. (2018) Points of significance: Curse(s) of dimensionality Nature Methods 15:399–400.