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disease: not obvious

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

Genes that make us sick

It is said that for money you can have everything, but you cannot. You can buy food, but not appetite; medicine, but not health; knowledge, but not wisdom; glitter, but not beauty; fun, but not joy; acquaintances, but not friends; servants, but not faithfulness; leisure, but not peace. You can have the husk of everything for money, but not the kernel.
— Arne Garborg

I have recently had the opportunity to contribute to The Objects that Power the Global Economy, a book by Quartz.

The book is about objects that have impact on our world and our lives. "Each chapter of this book examines an object that is driving radical change in the global economy: how we communicate, what we eat, the way we spend our money. The stories are told through global reporting, original photography and illustration by award-winning artists, contributions from business visionaries, data visualization, and interactive features." (Quartz).

where disease hides in the genome

My illustration is of the human genome with a focus on the genes that have been implicated in disease.

We have about 30,000 genes and about half of these play some role in disease.

You can peruse what we know about the connection between genetics and illness at the Online Mendelean Inheritance of Man database. For example, a cursory search for "cancer" results in over 3,500 entries.

It's important to realize that these aren't genes that cause disease—its misregulation and mutations in them that are associated with disease (causality is complicated).

the visualization

The illustration shows the genome as a single line, wound in an Archimedean spiral. Chromosomes 1–22 are shown binned into about 10,000 regions along the spiral. Regions that have genes associated with disease are marked with dots—the size of the dot shows how many such genes are found. Each region corresponds to about 286,000 bases.

We see that in about 73% of the 286 kb regions, there are no genes. In about 18% we see a single gene and in roughly 10% two genes or more.

$regions genes 7,321 0 1,812 1 556 2 221 3 85 4 93 5+$

Winding the genome up in a spiral creates a compact representation. Squishing a line onto a page can be tricky.

Luckily, space filling curves like the Hilbert curve are very efficient at doing this. I've previously shown the genome along a Hilbert curve for a Scientific American Graphic Science page.

the artwork

I show several versions of the illustrations below. In the book, the image is printed on a black background.

The human genome is shown as a spiral. Starting at the top with chromosome 1 and proceeding clockwise, each of the 10,087 dots corresponds to 286,000 bases, colored by chromosome. Within each dot, the number of genes in that region implicated in disease is shown by the size of the black circle. Chromosomes X and Y are not shown. (zoom)
The human genome is shown as a spiral. Starting at the top with chromosome 1 and proceeding clockwise, each of the 10,087 dots corresponds to 286,000 bases, colored by chromosome. Within each dot, the number of genes in that region implicated in disease is shown by the size of the black circle. Chromosomes X and Y are not shown. (zoom)
The human genome is shown as a spiral, starting at the top with chromosome 1 and proceeding clockwise. The spiral is formed by 10,087 segments that correspond to 286,000 bases each. Segments that contain genes implicated in disease are indicated by dots, sized by the number of genes. Chromosomes X and Y are not shown. (zoom)
The human genome is shown as a spiral, starting at the top with chromosome 1 and proceeding clockwise. The spiral is formed by 10,087 segments that correspond to 286,000 bases each. Segments that contain genes implicated in disease are indicated by dots, sized by the number of genes. Chromosomes X and Y are not shown. (zoom)
The human genome is shown as a spiral, starting at the top with chromosome 1 and proceeding clockwise. The spiral is formed by 10,087 segments that correspond to 286,000 bases each. Segments that contain genes implicated in disease are indicated by dots, sized by the number of genes. Chromosomes X and Y are not shown. (zoom)
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Optimal experimental design

Tue 31-07-2018
Customize the experiment for the setting instead of adjusting the setting to fit a classical design.

The presence of constraints in experiments, such as sample size restrictions, awkward blocking or disallowed treatment combinations may make using classical designs very difficult or impossible.

Optimal design is a powerful, general purpose alternative for high quality, statistically grounded designs under nonstandard conditions.

Nature Methods Points of Significance column: Optimal experimental design. (read)

We discuss two types of optimal designs (D-optimal and I-optimal) and show how it can be applied to a scenario with sample size and blocking constraints.

Smucker, B., Krzywinski, M. & Altman, N. (2018) Points of significance: Optimal experimental design Nature Methods 15:599–600.

Krzywinski, M., Altman, N. (2014) Points of significance: Two factor designs. Nature Methods 11:1187–1188.

Krzywinski, M. & Altman, N. (2014) Points of significance: Analysis of variance (ANOVA) and blocking. Nature Methods 11:699–700.

Krzywinski, M. & Altman, N. (2014) Points of significance: Designing comparative experiments. Nature Methods 11:597–598.

The Whole Earth Cataloguer

Mon 30-07-2018
All the living things.

An illustration of the Tree of Life, showing some of the key branches.

The tree is drawn as a DNA double helix, with bases colored to encode ribosomal RNA genes from various organisms on the tree.

The circle of life. (read, zoom)

All living things on earth descended from a single organism called LUCA (last universal common ancestor) and inherited LUCA’s genetic code for basic biological functions, such as translating DNA and creating proteins. Constant genetic mutations shuffled and altered this inheritance and added new genetic material—a process that created the diversity of life we see today. The “tree of life” organizes all organisms based on the extent of shuffling and alteration between them. The full tree has millions of branches and every living organism has its own place at one of the leaves in the tree. The simplified tree shown here depicts all three kingdoms of life: bacteria, archaebacteria and eukaryota. For some organisms a grey bar shows when they first appeared in the tree in millions of years (Ma). The double helix winding around the tree encodes highly conserved ribosomal RNA genes from various organisms.

Johnson, H.L. (2018) The Whole Earth Cataloguer, Sactown, Jun/Jul, p. 89

Why we can't give up this odd way of typing

Mon 30-07-2018
All fingers report to home row.

An article about keyboard layouts and the history and persistence of QWERTY.

My Carpalx keyboard optimization software is mentioned along with my World's Most Difficult Layout: TNWMLC. True typing hell.

TNWMLC requires seriously flexible digits. It’s 87% more difficult than using a standard Qwerty keyboard, according to Martin Krzywinski, who created it (Credit: Ben Nelms). (read)

McDonald, T. (2018) Why we can't give up this odd way of typing, BBC, 25 May 2018.

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.

Cover design for Apr 2018 issue of Molecular Case Studies. (details)

Happy 2018 $\tau$ Day—Art for everyone

Wed 27-06-2018
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.

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)