Giant virus discovery sparks debate over tree of life

Sara Reardon in Nature:

VirusEvolutionary biologists have never known what to make of viruses, arguing over their origins for decades. But a newly discovered group of giant viruses, called Klosneuviruses, could be a 'missing link' that helps to settle the debate — or provoke even more discord. In 2003, researchers reported that they had found giant viruses, which they named Mimiviruses, with genes that suggested their ancestors could live outside of a host cell1. The discovery split researchers into two camps. One group thinks viruses started out as self-sufficient organisms that became trapped inside other cells, eventually becoming parasitic and jettisoning genes they no longer needed. Another group views viruses as particles that snatched genetic material from host organisms over hundreds of millions of years. A study2 published on 6 April in Science provides evidence for the latter idea, that viruses are made up of a patchwork of stolen parts. But it has already sparked controversy and is unlikely to settle the raucous debate.

After the Mimivirus discovery, some researchers developed a theory that put viruses near the root of the evolutionary tree. They proposed that viruses comprised a ‘fourth domain’ alongside bacteria, eukaryotes — organisms whose cells contain internal structures such as nuclei — and bacteria-sized organisms called archaea. Mimiviruses, which at 400 nanometres across are about half the width of an E. coli cell and can be seen under a microscope, were unique in that they contain DNA encoding the molecules that translate RNA messages into proteins. Normal viruses make their host cells produce proteins for them. The team that discovered Mimiviruses thought the virus' ability to make their own proteins suggested that these viral giants descended from ancient free-living cell type that may no longer exist2. “They reinitiated the debate about the living nature of viruses, and of their relationship with the ‘cellular’ world,”

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Love on a New Continent

by Humera Afridi

I am the companion of the new Adam

Who has earned my self-assured love

(Fahmida Riaz)

“Mommy, when are you going to start dating? You’re not even trying!” complained my nine-year old on a sunny afternoon in February, two days before Valentine’s Day.

We’d just returned home from family day at Chelsea Piers, our cherished Sunday ritual. His words—incongruous in that moment and, certainly so, for his age—struck me with force. I dropped my gym bag, feigned horror. But the horror was as real as if I’d stumbled upon a nest of rodents as I breathed through a rush of emotions—alarm, sadness, mirth, shock.

These had suddenly appeared skittering and scampering, prodded by an innocent question which had penetrated, with the precision of an arrow, layers of social and cultural conditioning. My son’s words had spilled out, I noticed, in a single breath, question and complaint merged into an astutely observed assessment which he’d delivered with an air of impatience.

I threw my head back and laughed, pinched his chin. “Eeeks! Dating? I have zero interest. And, anyway, who has time?”

“Mom, there are apps, you know, where you can find a boyfriend.” He was adamant, unwilling to relinquish his position. “And that way I can have a stepdad,” he added, frowning now to conceal a tremor of self-consciousness.

This tragi-comic pronouncement in the elevator ride up to our apartment rapidly mounted into an existential crisis—I felt the urge to double over in reams of chronic laughter, I wanted to curl myself into a ball and weep, all at the same time.

Instead, I joked. “Hey, mister, how come you know about dating apps?”

The ground beneath my feet felt like quicksand. The mellow passage of domestic stability was suddenly under threat with the possibility of the new order that my son’s unsolicited and precocious ‘advice’ had raised. Stendhal’s words popped into my mind: “The most surprising thing of all about love is the first step, the violence of the change that takes place in a man’s mind.” Presumably, a woman’s mind, too. And I, comfortably ensconced in my routines, freedom, and independence desired no disruption, thank you. Motherhood is a gift I cherish; it has also, naturally, been my compass. But my child had now inadvertently made lucid the fact that I’d been occupying this station complacently, with inordinate fealty to an ideal of motherhood that upholds those who are settled in constancy, those spared the volatility and “violence” of new love—married mothers.

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TRIGGERNOMETRY: NEW ANGLES IN PROGRESSIVE THOUGHT

by Richard King

USMC-120503-M-9426J-001Good news for US exports this month. Australia, my adoptive country, has also adopted the trigger warning. Taking its lead from US campuses, Melbourne's Monash University has obliged its academic staff to review their course materials with the aim of identifying content that may be "emotionally confronting" for students, and is set to attach fifteen advisory statements to subjects dealing with, inter alia, racism, torture, homophobia and colonialism. All very exotic in a country revered for its colourful language and casual racism, but that's the power of globalisation. And they say the American Century is over.

Not everyone is happy about the new arrival. Following their US counterparts (the reaction, too, has an imported feel), critics of "political correctness" have declared the adoption of trigger warnings to be a new front in the culture wars and the heir to such PC atrocities as affirmative action and university speech codes. According to this line of argument, trigger warnings are a Trojan horse from which the polo-necked Foucauldian foot-soldiers will emerge the moment Professor Tomnoddy brandishes his Amontillado-stained copy of Tractatus Logico-Philosophicus. "Sensitivity" is code for censorship and the imposition of radical values on the entire academic cohort.

Notwithstanding the muscular, male-menopausal, almost vaudevillian liberalism with which their animadversions come served, these critics aren't completely wrong. Trigger warnings are political and do derive, via a circuitous route, from the cultural "turn" in leftwing politics in the late 1960s and 1970s. But they are not political in the way conservatives or classical liberals think they're political, being neither an assault on "academic freedom" nor a Marcusean attempt to drive the sacred cows of tradition, "Western Civ." etc. towards the abattoir of Cultural Marxism. Possibly there's a bit of that, but my strong sense is that what we're dealing with here is a new form of subjectivity that regards the expression of personal hurt, not just as a form of political agency, but as the very stuff of politics itself. Like their close cousins "safe spaces" and "microaggressions", trigger warnings represent a new political epistemology.

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Comparing black ravens and ‘grue’

by Carl Pierer

Black raven

I.

The old problem of induction raised the question of how we can justify inferences from singular observations to general statements. In the last century two newer problems were presented. The Ravens Paradox, which I will explain in section II, is due to Carl G. Hempel. The ‘grue problem' was put forth by Nelson Goodman and I shall present it in section III. In section IV I will first compare the two problems and then attempt to show that Hempel's paradox can be solved, whereas Goodman's ‘grue' points to a deeper problem.

II.

Carl Hempel focuses on the question of what counts as evidence for hypotheses. There are two principles of inductive reasoning that we seem to accept.

(i) If all Ps have been observed to be Qs, then this counts as evidence for "All Ps are Qs". Hempel writes: "(…) this hypothesis is confirmed by an object a if a is P and Q; and the hypothesis is disconfirmed by a if a is P, but not Q." (Hempel 1945, p. 18)

(ii) What counts as evidence for one statement, counts as evidence for all logically equivalent statements. So, if all non-B's have been observed to be non-A's, then this counts as evidence for the original statement. It seems plausible to accept the second principle. The statements are equivalent exactly because they are true under the same conditions.

Hempel thinks that this account entails a paradox, namely the Ravens Paradox. Say we start off with the hypothesis: "All ravens are black". We can then construct its logical equivalent: "All non-black things are non-ravens". By (i), everything that we can observe that is not a raven and not black will count as evidence for the second statement. By (ii) we are bound to accept these evidences as evidence for the initial hypothesis. But this seems absurd. We do not believe that my brown jumper does in any way affect the hypothesis that all ravens are black. This fact seems completely irrelevant.

III.

Nelson Goodman formulated a "new riddle of induction". In order to construe it, he needs to come up with a new predicate: the infamous "grue" (Goodman 1954, p 74). Objects are grue if they are observed before time t and are green, and if they are observed after t and they are blue. Now, t is some time in the future, say the 1st November 2020. So, if we have a green emerald before time t, then this certainly supports the hypothesis "All emeralds are green". However, we can also take it as evidence for "All emeralds are grue". The issue, then, is to determine whether we have any reasonable grounds to prefer thinking of emeralds as green over emeralds as grue.

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Critique of the Smiley Face

by Emrys Westacott

The ubiquitous yellow smiley is the perfect representation of our culture's default conception of happiness. It signifies a pleasant internal state of mind. Right now, life is fun, it says. I'm enjoying myself. Don't worry–be happy. Unknown

This is a subjectivist conception of happiness. It's all about how one feels, and it tends to be applied to relatively short periods of time: minutes, hours, days.

When discussing happiness with my students, I sometimes describe Barney the Couch Potato. Barney inherited enough money not to have to work for a living. He spends the bulk of his days lounging on the sofa playing video games, watching reruns of old TV sitcoms, smoking weed (it's legal where he lives), and drinking a few beers. He gets off his sofa just enough to stay more or less healthy. Friends drop by often enough to keep him from feeling lonely.

Is Barney happy? When I ask my students this question, nine out of ten invariably say yes. "Maybe I wouldn't want to live like that," they say, "but hey, if that's what he wants, and it makes him feel good, then I guess he's happy."

This response supports my suspicion that a subjectivist conception of happiness is dominant these days, at least in the US. What else could happiness be, after all, but lots of pleasure without too much pain? And what is pleasure if not an enjoyable subjective state?

One way of gaining a critical perspective on this view of happiness is to contrast it with the view of happiness found in ancient Greek philosophy, particularly in the thought of Plato, and Aristotle. Interestingly, their more objectivist notion of happiness, while it has been somewhat displaced, is still with us to some extent; so what they say does not sound utterly alien. Let's consider what it involves.

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Somewhere in Europe

by Holly A. Case

Bp-demonstration-Apr 9

Demonstration in Budapest in support of CEU, April 9, 2017

On Tuesday of last week, the Hungarian parliament passed a law that seeks to drive the Central European University, founded in 1991, out of the Hungary. Many articles and op-eds have been written condemning the law, and declarations of support have come from Hungarian universities and student unions, scores of universities and scholarly organizations in Europe and the US, and from CEU students and alumni. Demonstrations and solidarity events have taken place in Budapest, New York, London, Lisbon, Friedrichshafen, St. Petersburg, Warsaw, Saarbrücken, Amsterdam, Barcelona, Paris, Bucharest, Mainz, Vienna, Berlin, Cluj, Stockholm, Heidelberg, Zagreb, and Prague. Members of the European Parliament, as well as US and European diplomats and statesmen have criticized the law, all to no avail. The governing party in Hungary, Fidesz, with Prime Minister Viktor Orbán at its head, remains unmoved.

Somewhere in between all the domestic and international support and the Hungarian government's attacks on CEU is the actual place and the people who have studied or worked there. What follows is a series of anecdotes about an educational institution in the heart of Europe like no other, one that has no obvious forerunners or successors. The child of a euphoric moment in the region's history (1989), CEU has since grown and changed, but has also transformed the many people who have passed through it.

1996: The Conference (by yours truly, no affiliation with CEU)

I first visited CEU in the spring of 1996. A friend of mine and I had come up from the town of Szeged for a conference. We met the other participants in a cafeteria-like setting at the brand new Kerepesi dormitory on the outskirts of Budapest. The conditions for language surfing were ideal. Everyone had a few, it seemed: all the former Soviets knew Russian, all the former Yugoslavs knew…well, that language that they all spoke (the name of which was a plaything in that cafeteria, but a minefield outside it; the war in Bosnia had barely ended). Plus there were the displacement stories, like Leonid, a Russian-speaking Jew from Moldova, who also happened to speak Bulgarian as well as that language, thanks to friendships and a love interest from Serbia.

I gave my conference presentation on absurdism in Polish and Hungarian literature. While the cafeteria conversations had unfolded in numerous languages, the conference proceedings were all in English, which was rough for many of the participants who had only been learning the language for a short time. After my panel, a group of us—myself, a Croat, a Latvian, a Hungarian, and Leonid—were standing in the lobby when someone commented on how good my English was. “How did you learn it so good?” he wondered. Before I could tell him it was my native language, the Latvian spoke for me, waving a hand dismissively: “You know how it was, the borders were changing so quickly.”

We burst out laughing. The collapse of multi-national states, the fall of the Berlin Wall, and the end of the bipolar world order: the borders had indeed changed very quickly.

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Every story I have read about Trump supporters in the past week

Since Donald Trump’s approval rating now looks like something that got stuck to the bottom of my shoe, I joined the flood of journalists who went to Real America to gloat see how the Trump supporters are getting along.

Alexandra Petri in the Washington Post:

ImrsIn the shadow of the old flag factory, Craig Slabornik sits whittling away on a rusty nail, his only hobby since the plant shut down. He is an American like millions of Americans, and he has no regrets about pulling the lever for Donald Trump in November — twice, in fact, which Craig says is just more evidence of the voter fraud plaguing the country. Craig is a contradiction, but he does not know it.

Each morning he arrives at the Blue Plate Diner and tries to make sense of it all. The regulars are already there. Lydia Borkle lives in an old shoe in the tiny town of Tempe Work Only, Ariz., where the factory has just rusted away into a pile of gears and dust. The jobs were replaced by robots, not shipped overseas, but try telling Lydia that. (I did, very slowly and patiently, I thought, but she still became quite brusque.) Her one lifeline was an Obama-era jobs training program, but she says that she does not regret her vote for Trump and likes what he says about business. She makes a point of telling me that she is not racist, but I think she probably is, a little.

Next to her sits Linda Blarnik. Like the rusty hubcaps hanging on the wall behind her, she was made in America 50 years ago, back when this town made things, a time she still remembers fondly. She says she has had just enough of the “coastal elitist media who keep showing up to write mean things about my town and my life, like that thing just now where you said I was like a hubcap, yes you, stop writing I can see over your shoulder.” Mournfully a whistle blows behind her, the whistle of a train that does not stop in this America any longer.

More here.

New insight into proving math’s million-dollar problem: the Riemann hypothesis

Lisa Zyga in Phys.org:

ScreenHunter_2664 Apr. 09 19.29Researchers have discovered that the solutions to a famous mathematical function called the Riemann zeta function correspond to the solutions of another, different kind of function that may make it easier to solve one of the biggest problems in mathematics: the Riemann hypothesis. If the results can be rigorously verified, then it would finally prove the Riemann hypothesis, which is worth a $1,000,000 Millennium Prize from the Clay Mathematics Institute.

While the Riemann hypothesis dates back to 1859, for the past 100 years or so mathematicians have been trying to find an operator function like the one discovered here, as it is considered a key step in the proof.

"To our knowledge, this is the first time that an explicit—and perhaps surprisingly relatively simple—operator has been identified whose eigenvalues ['solutions' in matrix terminology] correspond exactly to the nontrivial zeros of the Riemann zeta function," Dorje Brody, a mathematical physicist at Brunel University London and coauthor of the new study, told Phys.org.

What still remains to be proven is the second key step: that all of the eigenvalues are real numbers rather than imaginary ones. If future work can prove this, then it would finally prove the Riemann hypothesis.

More here.

Trees Have Their Own Songs and a new book by David George Haskell invites us to listen

Ed Yong in The Atlantic:

ScreenHunter_2663 Apr. 09 19.20Just as birders can identify birds by their melodious calls, David George Haskell can distinguish trees by their sounds. The task is especially easy when it rains, as it so often does in the Ecuadorian rainforest. Depending on the shapes and sizes of their leaves, the different plants react to falling drops by producing “a splatter of metallic sparks” or “a low, clean, woody thump” or “a speed-typist’s clatter.” Every species has its own song. Train your ears (and abandon the distracting echoes of a plastic rain jacket) and you can carry out a botanical census through sound alone.

“I’ve taught ornithology to students for many years,” says Haskell, a natural history writer and professor of biology at Sewanee. “And I challenge my students: Okay, now that you’ve learned the songs of 100 birds, your task is to learn the sounds of 20 trees. Can you tell an oak from a maple by ear? I have them go out, pour their attention into their ears, and harvest sounds. It’s an almost meditative experience. And from that, you realize that trees sound different, and they have amazing sounds coming from them. Our unaided ears can hear how a maple tree changes its voice as a soft leaves of early spring change into the dying one of autumn.”

More here.

‘Unwanted Advances’ Tackles Sexual Politics in Academia

Jennifer Senior in the New York Times:

06BOOKKIPNIS1-articleInline-v2Read enough stories about the madness whipping through college campuses right now, and you can’t help but wonder if our institutions of higher learning have put the “loco” in in loco parentis. There was once a time when America’s students and faculty were united in their desire to defend their free-speech prerogatives, but no longer: Universities are now hypervigilant about protecting students from ideas that might be considered offensive or traumatizing, and many students are hyper-assertive in their demands to be protected from them.

I do not want to reduce the turbulence on today’s college campuses to caricature. (Though last month’s flare-up at Middlebury, which turned a planned colloquy into a crime scene, makes for a pretty fat target.) Those who defend trigger warnings, safe spaces and “empathetic correctness” have reasons for doing so, and no one wants vulnerable young people to experience gratuitous suffering.

But it’s also hard to ignore the irony here: Universities are now terrible places to find political heterogeneity. Campus discourse has become the equivalent of the supermarket banana. Only one genetic variety remains.

Among the educators who recently found herself at the treacherous intersection of free speech and sensitivity politics is Laura Kipnis, a film professor, cultural critic and dedicated provocateur at Northwestern University. Responding to a new campus directive that prevented professors from dating undergraduates, she wrote an essay for The Chronicle of Higher Education in February of 2015 entitled “Sexual Paranoia Strikes Academe.” Within days of publication, she was brought up on Title IX complaints for creating a “hostile environment.” She spent 72 days in the public stockade for it, until the university cleared her of any wrongdoing.

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new ground on counseling survivors of trauma, sexual assault

From EurikAlert!

ProfCommunication studies Associate Professor Christina Yoshimura teaches courses in interpersonal communication, and her research focuses on how personal relationships intersect with larger systems, such as health care or the workplace. Yoshimura also volunteers as a clinical mental health counselor at UM's Curry Health Center Counseling Services in order to bring research out of academia and into the daily lives of students at UM.

…"In our culture there are so many things we give people specific teaching in, like how to calculate the circumference of a circle or how to drive a car," she said. "Yet even though we know from countless research studies that good relationships are essential to our health and well-being, and even though we know many communication behaviors that are correlated with healthy relationships, it is rare to find any of that taught to people outside of select university classes." For example, people often struggle to start a conversation with someone new, or handle conflict effectively. Yoshimura's practice-based counseling allows students to get an overview of productive relational communication skills and then practice them with one another. "This incorporates cognitive understanding of the skill with the repeated physical experience of using the skill," Yoshimura said. "Most people have room to improve their social functioning, and could experience less anxiety and more satisfying interpersonal interactions with even just a little practice." "I see communication as a powerful frame for understanding and improving our human experiences," she said. "Participating on the Department of Justice grant was deeply meaningful to me as a way of seeing, serving and respecting sexual assault survivors on campus. This is of the utmost importance here at UM, and it's also an issue of national importance. Providing an avenue for students to develop and refine their skills in building positive relationships is another way to serve the students on our campus. "Using the social science research in interpersonal communication to work directly in the lives of our students is an immense privilege," Yoshimura said, "and the obligation to do that well will continue to guide my choices here at the University and within our Missoula community."

More here.

The World Is Getting a Lot More Authoritarian: anyone born in 2016 will be less free than someone born during the 1990s

Brian Klaas in Alternet:

Shutterstock_567561736For the first time since the end of the Cold War, the world is losing faith in democracy. Between Donald Trump’s rise in American politics and the predictable but self-inflicted "Brexit" economic shockwave, many are now openly asking what was previously an unthinkable question in the West: can people really be trusted with self-government? Is it time to ditch democracy and try something else? After the Soviet Union fell, democracy expanded at an unprecedented rate. Today, global democracy has receded slightly every year since 2006; in other words, there has been no democratic forward progress for the last decade. At the other end of the spectrum, powerful authoritarian regimes are becoming more authoritarian. Across multiple indexes and measures, democracy is steadily declining at worst and stagnating at best. Unless the trend is reversed, anyone born in 2016 will be, on average, less free than someone born during the 1990s. These declines are not an accident; they are the battle scars of a struggle between the rule of the people and the rule of despots and dictators. Right now, the people are losing.

However, the democratic sky is not falling. The world remains more democratic than it has been at almost any time in human history. Many countries that were bastions of authoritarian repression just a few decades ago are now democracies. Nonetheless, the recent retreat of democracy is serious cause for concern. This is not a theoretical philosophical debate. Billions of people remain trapped in unresponsive, unaccountable regimes where ruthless oppression is common. As many despots have rolled back democracy or refused to embrace it, they have found an unlikely accomplice: the West. Western governments, in London, Paris, Brussels, and most of all Washington, have directly and indirectly aided and abetted the decline of democracy around the globe. This unfortunate truth comes despite the stated goals of all Western governments and despite the personal principles of almost everyone in those governments. Overwhelmingly, Western elites genuinely believe in democracy. They want democracy to spread. Moreover, Western governments have been, are, and will continue to be the biggest force backing democracy in the world. But their current approach is backfiring. … For the moment, though, the West is suffering an acute case of democracy promotion fatigue. Its leaders have less of a stomach for the short-term risks it presents than they used to.

More here.

Sunday Poem

My Father Holds the Door for Yoko Ono

In New York City for a conference
on weed control, leaving the hotel
in a cluster of horticulturalists,
he alone stops, midwestern, crewcut,
narrow blue tie, cufflinks, wingtips,
holds the door for the Asian woman
in a miniskirt and thigh high
white leather boots. She nods
slightly, a sad and beautiful gesture.
Neither smile, as if performing
a timeless ritual, as if anticipating
the loss of a son or a lover.

Years later, Christmas, inexplicably
he dons my mother’s auburn wig,
my brother’s wire-rimmed glasses,
and strikes a pose clowning
with my second hand acoustic guitar.
He is transformed, a working class hero
and a door whispers shut,
like cherry blossoms falling.
.

by Christopher Chambers
from Folio, Winter 2004

.

weighing goods and people: ethics out of economics: rationality through reasoning…and climate change

9780631199724

Richard Marshall interviews John Broome in 3:AM Magazine:

3:AM: Economics has recently been accused ( see Amitai Etzioni in‘Evonomics’) of leading to unethical, anti-social thinking so do you think economics needs an ethical theory? If it does, which one?

JB: ‘Of course it does’. Economists constantly make recommendations about all sorts of things, from how the banking system should be organized to what should be done about climate change. What sort of ‘should’ is that? There are non-ethical ‘shoulds’, such as the way you should hold a golf club. But the economists’ ‘should’ always involves balancing the conflicting interests of different people against each other. This makes it inevitably a matter for ethics. Since it is engaged in ethics, economics needs ethical theory to do its work well.

These days many economists deny this. They are so thoroughly immersed in their own ethical assumptions that they don’t recognize them for what they are. The explicitly ethical branch of economics is known, oddly, as ‘welfare economics’. When I was a student in economics around 1970, we were taught serious welfare economics, including such topics as the value of equality and the theory of ‘optimal taxation’. But soon after that, welfare economics stopped being taught in most US universities, and a generation grew up in ignorance of it.

It was this ignorance that drew me back to work with economists ten years ago. At the start of ‘The Stern Review of the Economics of Climate Change‘ the economist Nicholas Stern announced that his work rested on ethical premises, and he would state what they were. His report drew strong criticism from some US economists, who claimed that ethical premises had no place in economics. I was incensed. I was by then a moral philosopher and not an economist, but I could not let economists propagate their own ethical views whilst pretending they were not ethical views at all. So I found myself once again working with economists on climate change, to try and make sure they recognized their ethical premises.

More here.

‘IMAGINARY CITIES’ BY DARRAN ANDERSON

Imaginary-citiesJoseph Schreiber at The Quarterly Conversation:

Unlike the standard guidebook, Anderson offers his traveler no pictures, maps, or diagrams. This is intentional. Side trips are encouraged as the fancy strikes, and generous footnotes are provided for those who wish to follow up on quotes and references. (Of course, there is also the ease of stopping into Google for quick access to an image, biography, or further background material.) Anderson’s extended essay feels like spending time with an entertaining, well-read explorer who has traversed the cities of the imagination and returned with exotic tales that stretch back into pre-history and out into the solar system. We are in the presence of a modern-day Marco Polo who understands that “all cities can, and should be read.” His aim is to help us learn to trace these narratives ourselves.

Our guide is an Irish writer living in Scotland. He is neither an academic nor an architect, but his focus of attention lies in the intersection of culture, architecture, and technology. In a recent podcast, Anderson traced the genesis of this project to long-standing fascinations with cities and with the point at which reality and myth meet. As he became increasingly obsessed with architects and started looking through their plans, he found that beyond their iconic structures, each had drafted countless schemes and designs that would remain, for a variety of reasons, unrealized. With a different set of circumstances, then, the skylines and urban landscapes we know now could have been very different—as they once were in the past and will be in the future. The modern city is in flux and can perhaps best be understood only through a shifting kaleidoscope of angles and perspectives.

more here.