This Friday, June 21, 2013 is NSA whistleblower Edward Snowden’s 30th birthday and there’s a worldwide solidarity party going down at a time and public place of your choosing. Here are a few ideas to help you celebrate.

Surveillance Cupcakes

How about these eye-catching cupcakes?

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Say Cheese!

Get a small magnetic board and some alphabet fridge magnets, then get people to spell out their birthday wishes. Snap a picture and upload to your favourite information-sharing portal.

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Mask-erade

Turn some heads and stay safe from state surveillance by concealing your identity under a costume.

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Non-Molotov Cocktails

Spice up your favourite mixed drink with a home-made cocktail umbrella. Just download the templates and print. Cut out the circles, tape to make a cone and stick on the end of a toothpick or skewer.

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Make some noise

It’s not a party without some tunes so bring some amplified music or instruments to make your own.

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If you’ve been anywhere near the news lately I’m sure you’re familiar with Steubenville. I’ve been blogging about the situation unfolding around the rape of a young girl last summer – the ensuing investigation, finger-pointing, Occupation, lawsuits, trial, convictions and public and media reactions – for six months now and the underlying issues just won’t go away.

I’m compelled to write today because of the recent controversy caused by tennis star Serena Williams’ comments in a Rolling Stone article and her subsequent apology. Serena Williams is the number-one tennis player in the world. In the article, she is described as “the most dominant figure in sports today”. I wonder about her sense of perspective from her now-priveliged position.

"Lots of my friends have been telling me lately that I’m spoiled," Serena says with a baffled look on her face. "And I’m like, ‘Really? I’m not spoiled.’"

Let’s take a look at what she actually said:

"Do you think it was fair, what they got? They did something stupid, but I don’t know."

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I was stunned to find out that the activist responsible for initiating #OpRollRedRoll – essentially a publicity campaign in support of the Steubenville Jane Doe – had been raided by a SWAT team and was under investigation by the FBI. Stunned, but perhaps not surprised.

The man known to me previously under various online aliases as KYAnonymous has since been named as Deric Lostutter, a 26-year-old from Winchester, Kentucky. According to his story, he potentially faces a sentence that could eclipse those being served by the rapists he helped to expose.

I choose my words carefully here because I do not want to perpetuate the myth that the rape only came to light through the alleged hacking exploits of KYAnonymous and JustBatCat (because it did not) or through Alexandria Goddard’s blogging (because it did not).

Yes, there was hacking: a website in connection with the local high-school football team was temporarily defaced then knocked offline; some email accounts (notably that of the fan website’s administrator, Jim Parks) were hacked and the contents leaked and publicised.

And yes, blogging and tweeting helped to spread awareness about the case and stimulated a global debate about rape culture with a focal point in the USA.

And now, Deric Lostutter is the first of the “good guys” to take a hit.

Again, I choose my words carefully here because I do not want to perpetuate the myth that there are “good guys” and “bad guys” when in fact there are simply people, who all do things that they and others perceive as being good or bad to varying degrees.

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(via arteehee)

Read:

Step 1 – Why Darwin is not the ultimate authority on evolution

Step 2 – What evolution says about God

Step 3 – “Survival of the fittest” and why evolution doesn’t always promote survival

Step 4 – Natural selection is not the only way evolution bears fruit

Step 5 – Natural selection is entirely random, leads to ever-greater complexity, limitlessly creativity, or violates the second law of thermodynamics

Life itself appears to be extraordinarily unlikely, yet here we are. As explained in Step 2, evolution itself says very little about how life came to be here in the first place. Evolution simply explains how life forms change over time under the influences of random mutations and selective pressures (see Step 3 & Step 4).

The mutations that drive these changes happen in a number of ways. The one we perhaps most associate with the word mutation is the one behind the powers of comic book superhero the Hulk. Bruce Banner, a shy genius scientist, first transforms into the Hulk after being irradiated by a gamma bomb he invented while saving a youth who had wandered onto the testing range.

Gamma rays (and other forms of radiation such as ultraviolet light) can indeed damage DNA in such a way that can cause mutations in the sequence of nucleotide building blocks that make up the genetic code. Chemicals such as carcinogens can also cause such changes. To understand the genetic code and how it can be broken we must understand that there are essentially two languages that sing the song of life.

One is the language of nucleic acids, by which we generally mean DNA and the related molecule, RNA. DNA stands for deoxyribonucleic acid, while RNA stands simply for ribonucleic acid. These molecules are made up of building blocks known as nucleotides, which contain special information-encoding components called nucleases (or just bases, for short).

The other language is that of proteins, which are essentially a huge class of molecules that act as machines and scaffolds throughout the living world. Proteins themselves are made up of building blocks known as amino acids. When you hear about hair, skin or nail treatments containing amino acids or things like silk or milk proteins, it’s because your hair, skin and nails are all built around protein scaffolds known as keratins, while milk and silk are both also largely composed of other proteins.

These amino acid building blocks string together in a sequence that folds up into a particular shape. Like any machine or scaffold, the shape it has is the key to what it does and how it does it. So the sequence of letters that make up the “word” of a protein spell out its distinctive shape.

The language of genes is nucleotides and the language of proteins is amino acids. The genetic code itself works in such a way that three nucleotide bases spell out one letter of the protein alphabet. Which letter it is depends on the order of bases in the nucleotide “triplet”. 

There are four bases to choose from (represented by the letters G, A, T and C in the image below) so we have 64 possible combinations. The protein alphabet only has 20 letters (since there are only about 20 amino acids that form building blocks for proteins) so some of the base “triplets” mean the same thing. We also need signals to start and stop decoding a message.

The genetic code

Read the wheel from the inside out to decode the triplets and find out which of the 20 amino acid letters is being encoded.

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When we talk about a mutation, what we mean is a mistake in the nucleotide language of bases that causes one triplet to suddenly become another.

Enough of these changes caused our unfortunate Banner to turn into the Hulk, or so the story goes. Apart from gamma rays and other radiation, mutations can also just happen spontaneously as a result of their chemistry. At the molecular level, our genetic information finds itself in an ever changing chemical environment. A number of chemical reactions, such as tautomerism, depurination and deamination can cause mutations to be introduced.

Part of this complex chemistry of life is the process of duplicating genetic information. This process is facilitated by special proteins called DNA polymerases.

In general, DNA polymerases are extremely accurate, making less than one mistake for every 100,000,000 nucleotides added. Some DNA polymerases even have the ability to proofread and can remove nucleotides to correct mismatched bases. However, other DNA polymerases are able to “read through” certain kinds of mutations, at the expense of accuracy in error-free regions. The overall result is that DNA replication and even maintenance processes can introduce mutations.

All these different sources of mutation have one thing in common: the mutations they produce are entirely random. But while mutation is random, which mutations survive is not.

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Read:

Step 1 – Why Darwin is not the ultimate authority on evolution

Step 2 – What evolution says about God

Step 3 – “Survival of the fittest” and why evolution doesn’t always promote survival

4. Everything is an adaptation produced by natural selection, or natural selection is the only means of evolution.

This misconception is easy to understand, given the misunderstandings around what we actually mean by “natural selection” and the related concept, “survival of the fittest”. Earlier, I wrote about what natural selection (also called purifying selection) is, and how it is one particular mechanism by which life can evolve.

There are also others:

Disruptive selection (also called diversifying selection) describes changes in population genetics in which extreme values for a particular trait are favored over intermediate values: the population becomes divided into two distinct groups. This evolutionary process is believed to be one of the main driving forces behind sympatric speciation (which we’ll come to later).

Directional selection occurs when a certain characteristic has a greater fitness than others, leading it to become more frequent. This process can continue until the characteristic is fixed and the entire population shares the fitter feature.

Stabilising selection (not to be confused with natural selection) lowers the frequency of characteristics that have a negative effect – that is, produce organisms of lower fitness. This process can continue until a particular characteristic is eliminated from the population. 

Finally, a number of forms of balancing selection exist, which maintain a characteristic at intermediate frequencies in a population. The image below illustrates some of these diverse mechanisms in terms of the distribution of a characteristic within a population.

Different changes in population genetics as a result of various selective pressures:

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We tend to assume that all characteristics of plants and animals are adaptations that have arisen through natural selection. In fact, many features we observe are neither adaptations nor the result of selection at all.

Much change is due to random genetic drift rather than positive selection; it could be called “survival of the luckiest”.

Genetic drift occurs because the features of a generation of offspring are a sample of those features in the parent population, and because chance has a role in determining whether a given individual survives and reproduces. In other words, genetic drift happens due to the effect of random sampling. The effect of random sampling and genetic drift is illustrated by the following experiment involving coloured beads. 

Random sampling and genetic drift:

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To simulate a single generation, we pick one bead at random from the original jar. Whatever colour the bead is, we take a new bead of the same colour and put it in the second jar (returning the original bead to the first jar). We do this until we have filled the second jar with the same number of beads.

By the time we have reached the fifth generation, there are no red beads left in the jar: the red characteristic has disappeared from the population. 

This is purely the effect of random sampling and genetic drift – no natural selection necessary.

Evolution also passes through “population bottlenecks” – random external events such as natural disasters that cause a sudden reduction in population size. Bottlenecks can result in radical changes in the frequencies of particular characteristics, completely independent of any kind of selection.

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There’s also a special kind of bottleneck known as the founder effect, which is illustrated by the following diagram:

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If the two founding populations are separated enough and for a long enough time, random mutations, genetic drift or selective pressures may act on them to create entirely distinct species. Again, there are various ways in which such separation can occur. Anything that interferes with or prevents the exchange of genetic information can cause such separation, so new species can even arise within the same geographic region via sympatric speciation.

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The apple maggot, Rhagoletis pomonella, may be currently undergoing sympatric speciation. Between 1800 and 1850, after apples were first introduced to North America, an apple-eating variant emerged from the hawthorn-eating maggot population. The apple-eating race no longer normally feeds on hawthorns, and the hawthorn-eating race does not normally feed on apples. This may be an early step towards the emergence of separate species.

So species evolve due to the accumulation of a number of different random events and natural selection is certainly not the only means of evolution. Moreover, not all evolutionary adaptations are beneficial. We can see that not everything is an adaptation produced by natural selection, but that characteristics arise through the interplay of various kinds of selective pressures and other forces such as genetic drift.

Read Step 5 – Why evolution isn’t random or irreducibly complex

Read:

Step 1 – Why Darwin is not the ultimate authority on evolution

Step 2 – What evolution says about God

3. “Survival of the fittest” justifies “everyone for themselves”, or evolution always promotes the survival of species.

"Survival of the fittest" is a concept often discussed in relation to evolution, but what does it actually mean?

The phrase originated as an alternative description of “natural selection”, so let’s first understand what that means. Wikipedia provides an excellent definition:

Natural selection is the gradual, non-random process by which biological traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution. The term “natural selection” was popularized by Charles Darwin who intended it to be compared with artificial selection, which is now called selective breeding.

Natural selection remains one of the cornerstones of the synthesis of ideas that encompass our modern understanding of evolution.

In order to discuss evolution, natural selection and “survival of the fittest”, we must first understand two important concepts in biology: genotypes and phenotypes.

We describe the genetic makeup of a cell, an organism, or an individual as it’s genotype. So when we talk about genotypes we are talking about unique collections of genetic information.

A phenotype is the composite of an organism’s observable traits: visible appearance, development, physiological properties, behavior, and the products of behaviour (a bird’s nest or human clothing, for example). Phenotypes arise from the interaction between a particular genotype and its environment.

Another important concept to grasp is that evolution and natural selection are not the same thing.

Evolution refers to an entire framework of understanding of how life evolves, and natural selection is one aspect of that understanding.

In other words, evolution can happen in various different ways and natural selection (also called purifying selection) is one particular mechanism by which life can evolve.

It’s easiest to explain natural selection in reverse, so we must begin by accepting three things:

  • Mutations happen.
  • Mutations can be reflected in an organism’s physical characteristics.
  • Natural selection acts on an organism’s physical characteristics.

The results of natural selection are that functional genetic features – such as genes or regulatory DNA sequences – are conserved over time. This happens because of selective pressure against any variations that have negative consequences for an organism.

We can see evidence of this in many places but histones are a great example. Histones are microscopic protein particles that act as spools for DNA and are thus vital for allowing large genomes to fit inside small cell nuclei. When we examine histones from different species, there is remarkably little variation. Histones have presumably reached a point where most mutations result in histones that are less-good spools for DNA and therefore less-good for being alive as that particular organism. Histone structures (and the genetic information that encodes them) have been conserved over time because they are so fundamentally important to being alive for all cells with a nucleus.

Only after the integration of Darwin’s theory of evolution with a complex statistical appreciation of Gregor Mendel’s ‘re-discovered’ laws of inheritance did natural selection become generally accepted as an explanation for how life can evolve.

 

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Natural selection and “survival of the fittest” are intended to be synonymous. Today, both are widely misunderstood. In particular, “survival of the fittest” is often used in a way that is incompatible with the original meaning intended by its first two proponents: Herbert Spencer (who coined the term) and Charles Darwin.

Spencer was a British polymath and philosopher, and a contemporary of Darwin’s, who first used the phrase after reading On the Origin of Species. Spencer penned Principles of Biology in 1864, drawing parallels between his own economic theories and Darwin’s biological ones:

"This survival of the fittest, which I have here sought to express in mechanical terms, is that which Mr. Darwin has called ‘natural selection’, or the preservation of favoured races in the struggle for life."

Indeedoriginally – and perhaps more accurately – the phrase used was:

"survival of the best fitted".

Where Spencer coined the phrase as an analogy for natural selection in the context of economics, Darwin then borrowed it to describe biology again in later editions of On the Origin of Species. It is not a scientific description, but a metaphorical one:

"survival of the better adapted for immediate, local environment".

"Fitness" in this sense bears no relation to physical fitness. The "fittest" can be the most loving and selfless, not the most aggressive, selfish or physically capable. In fact, the term "fitness" has a very distinct definition within the context of evolutionary biology.

We can discuss the fitness of a given individual, or of a particular characteristic or trait. We can also discuss the fitness of a population or even an ecosystem. Fitness is often defined as a probability or a tendency for reproduction, rather an actual number of offspring. The reason for this is illustrated by a quote by evolutionary biologist John Maynard Smith:

"If the first human infant with a gene for levitation were struck by lightning in its pram, this would not prove the new genotype to have low fitness, but only that the particular child was unlucky."

So when we talk about the evolutionary fitness of populations or particular traits within them, we must talk in the language of mathematics, statistics and probabilities. Luckily, there are easier ways to do this than with equations and formulas.

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Read Step 1 – Why Darwin is not the ultimate authority on evolution

2. The theory of evolution says something about God, or evolution says something about how life came into being, or religion and evolution are incompatible.

This is a big myth, and it’s not hard to see why. Thinking about evolution raises lots of questions regarding the origins of life. Darwin himself struggled with the implications of his ideas and how they meshed with the religious doctrines of his time and his own personal beliefs. 

On the Origin of Species was published during the papacy of Pope Pius IX. The First Vatican Council was held in 1869, a decade after Darwin published his theory, and includes a section on faith and science:

"10. Not only can faith and reason never be at odds with one another but they mutually support each other, for on the one hand right reason established the foundations of the faith and, illuminated by its light, develops the science of divine things; on the other hand, faith delivers reason from errors and protects it and furnishes it with knowledge of many kinds."

Evolution doesn’t address God in any way, nor does it offer an explanation of how life came to exist in the first place. Those fall under the domains of theology and biopoiesis, respectively.

The theory of evolution simply offers a way to explain how genetic information propagates and results in the various life forms we see around us. 

Thus, evolution is only incompatible with certain beliefs in religious doctrine, not with the notion of divinity itself. This is perfectly illustrated by the following graphic, from The MIT Survey on Science, Religion and Origins, released at http://space.mit.edu/home/tegmark/survey.html in February, 2013.

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Read Step 3 – “Survival of the fittest” and why evolution doesn’t always promote survival

I think that there are a lot of misunderstandings about what evolution is, what ”survival of the fittest” means, and what Darwin has to do with it all (or is it that Dawkins guy?).

This post is my attempt to clear up some of the confusion.

So who was Charles Darwin and what exactly is his theory of evolution? Let’s begin to answer this question by examining some of the myths surrounding evolution that are propagated by people on both sides of the fence regarding evolution’s validity.

Here are some of the misconceptions that I’ve come across:

  1. Darwin is the ultimate authority on evolution, or Darwin’s theory of evolution is what we mean when we talk about evolution today.
  2. The theory of evolution says something about God, or evolution says something about how life came into being, or religion and evolution are incompatible.
  3. "Survival of the fittest" justifies "everyone for themselves", or evolution always promotes the survival of species.
  4. Everything is an adaptation produced by natural selection, or natural selection is the only means of evolution.
  5. Natural selection leads to ever-greater complexity, limitlessly creativity, or violates the second law of thermodynamics, or evolution is an entirely random process.
  6. Evolution produces creatures perfectly adapted to their environment and such beliefs as:
    • Evolution cannot explain traits such as homosexuality.
    • Accepting evolution undermines morality.
  7. Evolution is only a theory, or evolution cannot be disproved so is not science. Nobody has ever seen evolution happen and such questions as:
    • If humans came from apes, why aren’t apes evolving into humans?
    • If evolution is true, why are there so many gaps in the fossil record?

1. Let’s start with Darwin and his theory of evolution. I will show you why Darwin’s theory of evolution is not the same as the one we have today, and therefore why his theory is not the be-all-and-end-all of evolution.

However, before we begin, let’s take a little look at the evolution of evolution itself over the last 1000 years or so. 

Our timeline begins with the first detailed description of way certain diseases are inherited, followed by a long period in which plant breeders contributed much towards our understanding of inheritance. This understanding sparked some innovative ideas that continue to be refined into what we understand as the theory of evolution today.

 

The evolution of evolution

If you’re having trouble viewing the timeline you can also see it here

 

The eight-year-old Charles Darwin already had a taste for natural history and collecting when he joined the day school run by his Anglican preacher in 1817. At the age of 16, he spent the summer as an apprentice doctor before going to the University of Edinburgh Medical School.

Soon bored with his tutor’s course, Darwin neglected his medical studies in favour of the radical ideas of the Plinian Society, a student natural history group. Here Darwin was astonished by his mentor’s support for Jean Baptiste Lamarck’s ideas on the transmutation of species, after having read similar notions in his own grandfather’s journals.

Angered by the neglect of his studies, Darwin’s father sent him off instead to Christ’s College, Cambridge, for a Bachelor of Arts degree as the first step towards becoming an Anglican parson. In his final examination in January 1831 Darwin did well, coming tenth out of 178 candidates for the ordinary degree.

After graduating, the 22-year-old Darwin returned home on 29 August to find a letter proposing him as a suitable gentleman naturalist for a self-funded place on the HMS Beagle. Thus began a voyage that would lead Darwin to begin discrediting Lamarck’s theory of evolution in favour of his own.

It would take until 1859 for a 50-year-old Darwin to publish his ideas On the Origin of Species. They are meticulously worded: in the first edition of the book he makes a strong case for common descent, but avoids the controversial term “evolution”, which would be included  in later editions. His only allusion to human evolution was the understatement that:

"light will be thrown on the origin of man and his history."

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The Efé are a group of hunter-gatherer people living in the Ituri Rainforest of the Democratic Republic of Congo. Efé children often play a game known as Osani.

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You play Osani by sitting in a circle, feet touching, all connected. Each player in turn names a round object like the sun, the moon, a star, an eye  and then goes on to name a figurative expression of roundness the family circle, a baby in the womb, or the cycle of the moon. As players fail to come up with a circular term they are eliminated from the game until only one player remains. Tradition has it that this player will live a long and prosperous life, and it’s not hard to see how that could ring true.

This image is often shared in combination with the concept of ubuntu, a Bantu word for an African philosophy and way of life. Ubuntu has been explained in many different ways:

“Africans have a thing called ubuntu. It is about the essence of being human, it is part of the gift that Africa will give the world. It embraces hospitality, caring about others, being willing to go the extra mile for the sake of another. We believe that a person is a person through other persons, that my humanity is caught up, bound up, inextricably, with yours. When I dehumanize you, I inexorably dehumanize myself. The solitary human being is a contradiction in terms. Therefore you seek to work for the common good because your humanity comes into its own in community, in belonging.”

Archbishop Desmond Tutu

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A world of sheep and lambs, infiltrated by wolves, led by hawks, owned by fat cats, policed by pigs, being freed by rats, doves, owlslarks and bookworms.

I didn’t really want to write about Dzhokhar Tasarnaev, the only one of the two men accused of being the Boston Bombers still alive. His story is already being told elsewhere, by a wide variety of conflicting and contradictory sources. I didn’t want to write about him mainly because I have already published my thoughts on the Boston Marathon and the bombing.

Earlier, I wrote about turning things upside down. The same principle can be applied here. Dzhokhar is the man who did the Boston Bombings. Now upside down: the Boston Bombings were done by Dzhokhar, the man. Immediately the focus shifts from Dzhokhar-the-perpetrator to Dzkokhar-the-man. This provides two different frameworks within which Dzhokhar and the Bombings can be discussed. 

So I guess I won’t write about Dzhokhar, but instead I will write about Jahar, as he is known to his friends and supporters. Let me make one thing clear at this point: I do not support Jahar in the sense that I condone what he is accused of, nor do I think he is entirely innocent. However, I support Jahar’s rights as a human being in the same way that I support the rights of every other being on this planet. That includes the right to live.

Jahar violated that right for at least three people (four if we include his brother, Tamerlan, whom he allegedly ran over in a desperate bid to escape capture; and five if we include the MIT campus police officer, who he may or may not have shot). Whether this is simply the result of two angry young men or whether it was part of a larger operation involving the US government or other forces remains to be determined. It seems fairly clear at this point, from the crowd-sourced pictures in the public domain combined with the media narrative, that Jahar did – at least – position at least one bomb.

We condemn Jahar for his lack of compassion: how could he do such a thing? But should we not then turn the other cheek and show him compassion where he showed none? Should we not educate him in the ways of the world? Ways that – one would hope – are not just based on the philosophy of an eye for an eye?

Jesus himself forgave a mass-murderer, Saul of Tarsus, who was responsible for persecuting hundreds of Christians and who, around the age of 25, had an epiphany and converted himself to become Paul the Apostle. 

Without that act of forgiveness we would be down an Apostle; and the course of our collective history would be forever changed.

I recently had a confrontation with my younger cousin on Facebook. He was trying to make the point that rejoicing in any death is wrong (in reference to the recently deceased Margaret Thatcher). He chose to do so by posting a satirical statement rejoicing in the deaths of those killed in the attack at the Boston Marathon. I had to point out that when trying to make a point about discrediting a certain behaviour (like rejoicing in someone’s demise, or killing people, for example), it’s usually best to avoid using exactly the thing you are trying to discredit in your argument.

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"Look up."

This was a revelation, imparted to me by a friend during a difficult time in my life. Yet, he mean it literally. So, heeding his advice, every time I walked through the familiar streets around my home town, I looked up.

And you know what? I discovered a whole other city that had been hiding in plain sight. I discovered jokes and poetry scrawled high up on walls, art and architecture hidden from the eyes of ground-level gazers.

Looking up literally turned my world upside down.

Turning something upside down. It is perhaps the simplest of all mathematical transformations: a rotation of half a circle about a point. Yet turning something upside down is transformative in wholly different ways as well.

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