Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - contact me Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca on Twitter Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Lumondo Photography Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Pi Art Martin Krzywinski / Genome Sciences Center / mkweb.bcgsc.ca - Hilbertonians - Creatures on the Hilbert Curve
In your hiding, you're alone. Kept your treasures with my bones.Coeur de Piratecrawl somewhere bettermore quotes

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


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 2018 Pi Day art celebrates the 30th anniversary of `\pi` day and connects friends stitching road maps from around the world. Pack a sandwich and let's go!

`\pi` Approximation Day Art Posters


Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2018 `\pi` day shrinks the world and celebrates road trips by stitching streets from around the world together. In this version, we look at the boonies, burbs and boutique of `\pi` by drawing progressively denser patches of streets. Let's go places.

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2017 `\pi` day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` approximation day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Day 2014 Art Poster - Folding the Number Pi
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circular `\pi` art

The never-repeating digits of `\pi` can be approximated by 22/7 = 3.142857 to within 0.04%. These pages artistically and mathematically explore rational approximations to `\pi`. This 22/7 ratio is celebrated each year on July 22nd. If you like hand waving or back-of-envelope mathematics, this day is for you: `\pi` approximation day!

Want more math + art? Discover the Accidental Similarity Number. Find humor in my poster of the first 2,000 4s of `\pi`.
Vague mathematics and alternative explanations to reality ahead.
Equip your imagination.

What would circles look like if `\pi`=22/7?

Tiny loop, Folded dimensions and solidland

Imagine that the circle had a tiny loop at one of its points. The circumference of this loop would be added to the circumference of the circle, but the loop would be so small that we would never notice it.

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
In a universe where Pi=22/7, circles might have a single point at which another dimension is curled up, contributing to the additional component of circumference.

This is reminiscent of how string theories describe higher dimensions—as tiny loops at each point in space, except in my example the loop is only at one point.

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A 3rd dimension explained on a 2d plane. The 3rd dimension is represented by a circle of a very small radius.

This idea originated with Klein, who explained the fourth dimension as a curled up circle of a very small radius. Another way in which this curling-up is used is to say that the fifth dimension is a curled up Planck length, as explained in this Imagining 10 Dimensions video.

flatlanders and solidlanders

If this idea is difficult to wrap your head around, you're not alone. We cannot think of additional dimensions in the regular spatial sence since we have no means of experiencing such phenomena. We can however imagine how flatlanders might explain the 3rd dimension, since we can perceive it. They would draw the curled up circles in their plane because they would not have the experience of drawing with perspective mimicking our 3rd dimension.

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
How creatures that live in a 2-dimensional world, so-called flatlanders, might explain the 3rd dimension (left) and how we ourselves might visualize their explanation (right).

We would draw their explanation as shown on the right in the figure above, borrowing from our concept of the 3rd spatial dimension. Now imagine showing our explanation to a flatlander. They would not see the same thing as you—the circles would not intuitively imply the higher dimension to them.

This is analogous to why we cannot draw folded up dimensions. We are merely solidlanders—flatlanders in 3d space. Creatures that can perceive more spatial dimensions would use us as examples of diminished perceptual ability.

Did you notice the fallacy in the term solidlander? We refer to solids as objects that occupy the maximum number of spatial dimensions. There's no reason to think that creatures that perceive more dimensions wouldn't use this word the same way we do. We're solidlanders from our perspective and they're solidlanders from theirs.

relativistic speeds, frames of reference and length contraction

Another way to imagine how a circle might look is a little more realistic. The theory of special relativity tells us that when we travel at speed relative to another object the dimensions of that object appear contracted to us in the direction of motion.

This contraction is always present, but essentially imperceptible unless we're travelling fast enough. For example, in order for a 1 meter object to appear contracted by the length of a hydrogen molecule (0.3 nm) we would have to be travelling at 7.3 km/s (Wolfram Alpha calculation)!

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
If we travel at a speed of 0.04c and use the radius length along our direction of motion, the circumference of the circle will appear to be `2 \times 22/7 \times r`.

How fast would we have to be going to compress the circle sufficiently so that its circumference and radius ratio embody the `22/7` approximation of `\pi`? Pretty fast, it turns out. If we travel at just over 12,000 km/sec (0.04 times the speed of light, Wolfram Alpha calculation), the circle will compress as shown in the figure above, and the ratio of its circumference to the radius along direction of motion will make `\pi` appear to be `22/7`.

This compression in length would be barely perceptible to us. Below are both circles, shown overlapping, with `delta` being the extra length in radius required.

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deformation of the circle required to change the ratio of its circumference to original radius from \pi to 22/7.

The value of `\delta`, which is 0.0008049179155 (if `r = 1`), can be calculated by considering the perimeter of an ellipse. The fact that `\delta` is small shouldn't be surprising since `22/7` is an excellent approximation of `\pi`, good to 0.04%.

Calculating the parameter of an ellipse is more complicated than calculating it for a circle because it uses something called an elliptic integral. This integral has no analytical solution and requires numerical approximation. Luckily, we have computers.

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
If a circle compressed slightly in one direction (e.g. vertically) then we can make the ratio of its circumference to the new radius be 2 × 22/7.

We can use the expression shown above for the perimeter of the ellipse to determine how much the circle needs to be deformed. Let's write `a = r + \delta` (original radius with slight deformation `\delta`) and `b=r`. Since `22/7 > \pi` we know that `\delta > 0`.

It remains to solve the equation below for a value of `\delta` that will yield a ratio of circumference to `r` of `2 \times 22/7`.

Pi Approximation Day Art Poster / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The equation we need to solve to determine how much of a stretch the circle needs.

To make things simpler, let set `r=1`. Solving the equation numerically, I find $$\delta = 0.0008049179155$$

You can verify this solution at Wolfram Alpha.

the meaning of full-circle

After all this, we come full-circle to the meaning of full-circle.

You might ask why I didn't change the definition of `\pi` to `22/7` in the upper limit of the integral. After all, why not make the approximation exercise more faithful to the approximation?

It turns out that if I did that I would get `\delta=0`, which brings us back to the original circle. How is this possible?

Technically, this is because the integral returns the upper limit as its answer if the eccentricity is zero (i.e., `E(x,0)=x`).

Intuitively, this is because changing the upper limit of the integral actually redefines the angle of a full revolution. Now, full-circle isn't `2 \pi` radians, but `2 \times 22/7`. Given that the ratio of the circumference of a circle to its radius is exactly the size, in radians, of a full revolution, we don't need to change the shape of the circle if we're willing to change what a full revolution means.

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news + thoughts

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Background reading

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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
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.

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)