Trance opera—Spente le Stellebe dramaticmore quotes

# asking about questions is revealing

2020 $\pi$ day art and the piku

# visualization + design

“Transcendental Tree Map” from Yearning for the Infinite. This video premiered on 2020 Pi Day. Music by Max Cooper. Animation by Nick Cobby and myself.
The 2020 Pi Day art celebrates digits of $\pi$ with piku (パイク) —poetry inspired by haiku.
They serve as the form for The Outbreak Poems.
A $\pi$ day music video!: Transcendental Tree Map premieres on 2020 Pi Day from Max Cooper's Yearning for the Infinite. Animation by Nick Cobby and myself. Watch live from Barbican Centre.

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

2019 $\pi$ has hundreds of digits, hundreds of languages and a special kids' edition.
2018 $\pi$ day
2017 $\pi$ day
2016 $\pi$ approximation day
2016 $\pi$ day
2015 $\pi$ day
2014 $\pi$ approx day
2014 $\pi$ day
2013 $\pi$ day
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!

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.

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.

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.

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.

# The Outbreak Poems

Tue 24-03-2020

I'm writing poetry daily to put my feelings into words more often during the COVID-19 outbreak.

$Panic can wait for tomorrow.$
$Regrets live on curves not tangents.$
$Small chances are never zero.$
$Month's last day waits for another year.$

# Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses

Tue 17-03-2020

A poster full of epidemiological worry and statistics. Now updated with the genome of SARS-CoV-2 and COVID-19 case statistics as of 3 March 2020.

Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Bacterial and viral genomes of various diseases are drawn as paths with color encoding local GC content and curvature encoding local repeat content. Position of the genome encodes prevalence and mortality rate.

The deadly genomes collection has been updated with a posters of the genomes of SARS-CoV-2, the novel coronavirus that causes COVID-19.

Genomes of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
Ball of 56 SARS-CoV-2 coronaviruses that causes COVID-19.
The first SARS-CoV-2 genome (MT019529) to be sequenced appears first on the poster.

# Using Circos in Galaxy Australia Workshop

Wed 04-03-2020

A workshop in using the Circos Galaxy wrapper by Hiltemann and Rasche. Event organized by Australian Biocommons.

Using Circos in Galaxy Australia workshop. (zoom)

Galaxy wrapper training materials, Saskia Hiltemann, Helena Rasche, 2020 Visualisation with Circos (Galaxy Training Materials).

# Essence of Data Visualization in Bioinformatics Webinar

Thu 20-02-2020

My webinar on fundamental concepts in data visualization and visual communication of scientific data and concepts. Event organized by Australian Biocommons.

Essence of Data Visualization in Bioinformatics webinar. (zoom)

# Markov models — training and evaluation of hidden Markov models

Thu 20-02-2020

With one eye you are looking at the outside world, while with the other you are looking within yourself.
—Amedeo Modigliani

Following up with our Markov Chain column and Hidden Markov model column, this month we look at how Markov models are trained using the example of biased coin.

We introduce the concepts of forward and backward probabilities and explicitly show how they are calculated in the training process using the Baum-Welch algorithm. We also discuss the value of ensemble models and the use of pseudocounts for cases where rare observations are expected but not necessarily seen.

Nature Methods Points of Significance column: Markov models — training and evaluation of hidden Markov models. (read)

Grewal, J., Krzywinski, M. & Altman, N. (2019) Points of significance: Markov models — training and evaluation of hidden Markov models. Nature Methods 17:121–122.

### Background reading

Altman, N. & Krzywinski, M. (2019) Points of significance: Hidden Markov models. Nature Methods 16:795–796.

Altman, N. & Krzywinski, M. (2019) Points of significance: Markov Chains. Nature Methods 16:663–664.

# Genome Sciences Center 20th Anniversary Clothing, Music, Drinks and Art

Tue 28-01-2020

Science. Timeliness. Respect.

Read about the design of the clothing, music, drinks and art for the Genome Sciences Center 20th Anniversary Celebration, held on 15 November 2019.

Luke and Mayia wearing limited edition volunteer t-shirts. The pattern reproduces the human genome with chromosomes as spirals. (zoom)

As part of the celebration and with the help of our engineering team, we framed 48 flow cells from the lab.

Precisely engineered frame mounts of flow cells used to sequence genomes in our laboratory. (zoom)

Each flow cell was accompanied by an interpretive plaque explaining the technology behind the flow cell and the sample information and sequence content.

The plaque at the back of one of the framed Illumina flow cell. This one has sequence from a patient's lymph node diagnosed with Burkitt's lymphoma. (zoom)