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bible: exciting


EMBO Practical Course: Bioinformatics and Genome Analysis, 5–17 June 2017.


visualization + design

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 2017 Pi Day art imagines the digits of Pi as a star catalogue with constellations of extinct animals and plants. The work is featured in the article Pi in the Sky at the Scientific American SA Visual blog.

The art of Pi (`\pi`), Phi (`\phi`) and `e`


Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2017 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` approximation day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2016 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2015 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` approx day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2014 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
2013 `\pi` day

Pi Art Posters
 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Circular `\pi` art

Numbers are a lot of fun. They can start conversations—the interesting number paradox is a party favourite: every number must be interesting because the first number that wasn't would be very interesting! Of course, in the wrong company they can just as easily end conversations.

I debunk the proof that `\pi = 3` by proving, once and for all, that `\pi` can be any number you like!

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Willing to fight against unreason? Curious about the luminous and wary of the supernatural? If so, you might want to substitute Hitchmas for Christmas—it comes earlier and there's scotch.

Periodically I receive kooky emails from people who claim to know more. Not more than me—which makes me feel great—but more than everybody—which makes me feel suspicious. A veritable fount of crazy is The Great Design Book, Integration of the Cosmic, Atomic & Darmic (Dark Matter) Systems by R.A. Forde.

Look at the margin of error. Archimedes' value for `\pi` (3.14) is an approximation - not an exact value. Would you accept an approximation or errors for your bank account balance? Then, why do you accept it for `\pi`? What else may be wrong? —R.A. Forde

What else may be wrong? Everything!

religion—the original roundoff error

Here is a "proof" I recently received that π = 3. The main thrust of the proof is that "God said so." QED? Not quite.

Curiously the proof was sent to me as a bitmap.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The 'proof' that π is exactly 3. (zoom)

Given that it claims to show that π has the exact value of 3, it begins reasonably humbly—that I "may find this information ... interesting." Actually, if this were true, I would find this information staggering.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
The actual 'proof' from the handwritten book (pp. 18-19), where 'The inaccuracy of its value manifests itself'. Hmhmm. (zoom)

what's wrong with wrong math?

Because mathematics is the language of physical reality, there's only that far that you can go with wrong math. If you build it based on wrong math, it will break.

Given that math is axiomatic and not falsifiable, its arguments are a kind of argument from authority—the authority of the axioms. You must accept the axioms for the rest to make sense.

Religion also makes its arguments from authority—a kind of divine authority by proxy—though its "axioms" are nowhere as compelling nor its conclusions useful. Normally, the deception in religion's arguments from authority is not obvious. The arguments have been inocculated over time—amgiguity, hedging and the appeal to faith—to be immune to criticism.

When these arguments include demonstrably incorrect math, the curtain falls. The stage, props and other machinery of the scheme becomes apparent. Here you can see this machinery in action. Or, should I say, inaction.

no, π is not 3

If you're 5 years-old: (1) draw a reasonably good circle, (2) lay out a piece of string along the circle and measure the length of the string (circumference), (3) measure the diameter of the circle, (4) divide circumference by diameter. You should get a value close to the actual value of π = 3.14. If you're older, read on.

The book purports "real" (why the quotes?) life experiments to demonstrate that that π is 3. I'll take a look at one below, since it makes use of a coffee cup and I don't like to see coffee cups besmirched through hucksterish claims.

What appears below is a critique of a wrong proof. It constitutes the right proof of the fact that the original proof is wrong. It is not a proof that `\pi = 3`!

The proof begins with some horrendous notation. But, since notation has never killed anyone (though frustration is a kind of death, of patience), let's go with it. We're asked to consider the following equation, which is used by the proof to show that `\pi = 3`. $$ \sin^{-1} \Delta \theta^c = \frac{\pi}{6} \frac{\theta^{\circ}}{y}\tag{1} $$

where $$ \begin{array}{l} \Delta \theta^c = \frac{2\pi}{12} & \theta^{\circ} = \frac{360^\circ}{12} & y = \frac{1}{2} \end{array} $$

At this point you might already suspect that we're asked to consider a statement which is an inequality. The proof might as well have started by saying "We will use `6 = 2\pi` to show that `\pi = 3`." In fact, this is the exact approach I use below prove that `\pi` is any number. But let's continue with examining the proof.

Nothing so simple as equation (1) should look so complicated. Let's clean it up a little bit. $$ \sin^{-1} a = \tfrac{\pi}{3} b\tag{2} $$

where $$ \begin{array}{l} a = \frac{2\pi}{12} & b = \frac{360^\circ}{12} \end{array} $$

The fact that we're being asked to take the inverse sine of a quantity that is explicitly indicated to be an angle should make you suspicious. Although an angle is a dimensionless quantity and we can write $$ \sin^{-1}(\pi \; \text{rad}) = \sin^{-1}(\pi) = 0 $$

using an angle as an argument to `\sin()` suggests that we don't actually know what the function does.

If we go back to (2) and substitute the values we're being asked to use, $$ \sin^{-1} \tfrac{\pi}{6} = \tfrac{\pi}{3} 30 = 10 \pi \tag{3} $$

we get $$ 0.551 = 31.416 \tag{4} $$

That's as good an inequality as you're going to get. An ounce of reason would be enough for us to stop here, backtrack and find our error. Short of that, we press ahead to see how we can manipulate this to our advantage.

In the next step, the proof treats the left-hand side as a quantity in radians—completely bogus step, but let's go with it—and converts it to degrees to obtain $$ 0.551 \times \tfrac{360}{2 \pi} = 31.574 $$

Yes, we just multiplied only one side of equation (4) by a value that is not one. Sigh.

After committing this crime, the proof attempts to shock you into confusion by stating that $$ 31.574 \neq 31.416 $$

And, given that these numbers aren't the same—they weren't the same in equation (4) either, so the additional bogus multiplication by \(\tfrac{360}{{2 \pi}}\) wasn't actually needed‐the proof states that this inequality must be due to the fact that we used the wrong value for `\pi` in equation (1).

The proof fails to distinguish the difference between an incorrect identity (e.g. `1 = 2` is not correct) and the concept of a variable (e.g. `1 = 2 x` may be correct, depending on the value of `x`). Guided by the dim headlamp of unreason, it suggests that we right our delusion that `\pi = 3.1415...` and instead use `\pi = 3` in equation (1), we get $$ sin^{-1} \tfrac{1}{2} = 30 $$

which is true, because `\sin(30^\circ) = \tfrac{1}{2}`. Therefore, `\pi = 3`.

what just happened?

The entire proof is bogus because it starts with an equality that is not true. In equation (1), the left hand side is not equal to the right hand side.

a simpler wrong proof

To illustrate explicitly what just happened, here's a proof that `\pi = 4` using the exact same approach.

proof that π = 4

Consider the equation, $$ 4 = \pi \tag{5} $$

if we substitute the conventionally accepted value of `\pi` we find $$ 4 = 3.1415... $$

which isn't true! But if we use `\pi = 4` then $$ 4 = 4 $$

which is true! Therefore, `\pi = 4`. QED.

This only demonstrated that I'm an idiot, not that `\pi = 4`.

proof that π is any number you like

But why stop at 4? Everyone can have their own value of `\pi`. In equation (5) in the above "proof", set 4 to any number you like and use it to prove that `\pi` is any number you like.

Isn't misunderstanding math fun?

litany of horrors

The history of the value of π is rich. There is good evidence for `\pi = (16/9)^2` in the Egyptian Rhind Papyris (circa 1650 BC). Archimedes (287-212 BC) estimated `\pi \approx 3.1418` using the inequality `\tfrac{223}{71} \lt \pi \lt \tfrac{22}{7}`

One thing is certain, the precision to which the number is known is always increasing. At this point, after about 12 trillion digits.

So, it might seem, that `\pi \approx 3` is ancient history. Not to some.

Approximations are fantastic—they allow us to get the job done early. We use the best knowledge available to us today to solve today's problems. Tomorrow's problems might require tomorrow's knowledge—an improvement in the approximations of today.

`\pi = 3` is an approximation that is about 2,000 years old (not the best of its time, either). It's comical to consider it as today's best knowledge.

don't bring coffee cups into it

One of the "real" life experiments proposed in the book (pp. 65-68) uses a coffee cup. The experiment is a great example in failing to identify your wrong assumptions.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Don't abuse your coffee cup this way. (zoom)

First you take measurements of your coffee cup. The author finds that the inner radius is `r = 4 cm` and the depth is `d = 8.6 cm`. Using the volume of a cylinder, the author finds that the volume is either `412.8 \; \mathrm{cm}^3 \ 14.0 \mathrm \; {fl.oz}` if `\pi=3` or `432.3 \; \mathrm{cm}^3 = 14.6 \mathrm \; {fl.oz.}` if `pi=3.14...`.

You're next instructed to full up a measuring cup to 14.6 fl.oz. (good luck there, since measuring cups usually come in 1/2 (4 fl.oz) or 1/3 (2.6 fl.oz) increments).

The author supposedly does this and finds that he could fill the cup to the brim using only 13.7 fl.oz, with the remaining 0.9 fl.oz. spilling.

And now, for some reason, he concludes that this is proof that `\pi = 3`, despite that when using this value of `\pi` the cup's volume was calculated to be 14 fl.oz. not 13.7 fl.oz.

Other than being sloppy, it's most likely that the original assumption that the inside of the coffee cup is a perfect cylinder is wrong. The inside of the cup is probably smooth and perhaps even slightly tapered. Using the maximum radius and depth dimensions will yield a volume larger than the cup's. This is why water spilled out.

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news + thoughts

Tabular Data

Tue 11-04-2017
Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses.

After 30 columns, this is our first one without a single figure. Sometimes a table is all you need.

In this column, we discuss nominal categorical data, in which data points are assigned to categories in which there is no implied order. We introduce one-way and two-way tables and the `\chi^2` and Fisher's exact tests.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Tabular data. Nature Methods 14:329–330.

...more about the Points of Significance column

Happy 2017 `\pi` Day—Star Charts, Creatures Once Living and a Poem

Tue 14-03-2017


on a brim of echo,

capsized chamber
drawn into our constellation, and cooling.
—Paolo Marcazzan

Celebrate `\pi` Day (March 14th) with star chart of the digits. The charts draw 40,000 stars generated from the first 12 million digits.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
12,000,000 digits of `\pi` interpreted as a star catalogue. (details)

The 80 constellations are extinct animals and plants. Here you'll find old friends and new stories. Read about how Desmodus is always trying to escape or how Megalodon terrorizes the poor Tecopa! Most constellations have a story.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Find friends and stories among the 80 constellations of extinct animals and plants. Oh look, a Dodo guardings his eggs! (details)

This year I collaborate with Paolo Marcazzan, a Canadian poet, who contributes a poem, Of Black Body, about space and things we might find and lose there.

Check out art from previous years: 2013 `\pi` Day and 2014 `\pi` Day, 2015 `\pi` Day and and 2016 `\pi` Day.

Data in New Dimensions: convergence of art, genomics and bioinformatics

Tue 07-03-2017

Art is science in love.
— E.F. Weisslitz

A behind-the-scenes look at the making of our stereoscopic images which were at display at the AGBT 2017 Conference in February. The art is a creative collaboration with Becton Dickinson and The Linus Group.

Its creation began with the concept of differences and my writeup of the creative and design process focuses on storytelling and how concept of differences is incorporated into the art.

Oh, and this might be a good time to pick up some red-blue 3D glasses.

BD Genomics 3D art exhibit - AGBT 2017 / Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A stereoscopic image and its interpretive panel of single-cell transcriptomes of blood cells: diseased versus healthy control.

Interpreting P values

Thu 02-03-2017
A P value measures a sample’s compatibility with a hypothesis, not the truth of the hypothesis.

This month we continue our discussion about `P` values and focus on the fact that `P` value is a probability statement about the observed sample in the context of a hypothesis, not about the hypothesis being tested.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Interpreting P values. (read)

Given that we are always interested in making inferences about hypotheses, we discuss how `P` values can be used to do this by way of the Benjamin-Berger bound, `\bar{B}` on the Bayes factor, `B`.

Heuristics such as these are valuable in helping to interpret `P` values, though we stress that `P` values vary from sample to sample and hence many sources of evidence need to be examined before drawing scientific conclusions.

Altman, N. & Krzywinski, M. (2017) Points of Significance: Interpreting P values. Nature Methods 14:213–214.

Background reading

Krzywinski, M. & Altman, N. (2017) Points of significance: P values and the search for significance. Nature Methods 14:3–4.

Krzywinski, M. & Altman, N. (2013) Points of significance: Significance, P values and t–tests. Nature Methods 10:1041–1042.

...more about the Points of Significance column

Snellen Charts—Typography to Really Look at

Sat 18-02-2017

Another collection of typographical posters. These ones really ask you to look.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Snellen charts designed using physical constants, Braille and elemental abundances in the universe and human body.

The charts show a variety of interesting symbols and operators found in science and math. The design is in the style of a Snellen chart and typset with the Rockwell font.

Essentials of Data Visualization—8-part video series

Fri 17-02-2017
Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca

In collaboration with the Phil Poronnik and Kim Bell-Anderson at the University of Sydney, I'm delighted to share with you our 8-part video series project about thinking about drawing data and communicating science.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Essentials of Data Visualization: Thinking about drawing data and communicating science.

We've created 8 videos, each focusing on a different essential idea in data visualization: encoding, shapes, color, uncertainty, design, drawing missing or unobserved data, labels and process.

The videos were designed as teaching materials. Each video comes with a slide deck and exercises.