Adonis Diaries

Archive for November 14th, 2013

What Makes the Beauty of a Butterfly? Organized Chaos?

Take a look at a butterfly’s wing, and you can learn a lesson about life.

Not that it’s beautiful, or fragile, or too easily appreciated only when it’s fading—though all that is true, and evident in a wing.

Look very close, at the edge of a pattern, where one color turns to another. The demarcation isn’t so abrupt as it seems at arm’s length. It’s not a line, but rather a gradient.

RANDON KEIM posted this JUN. 24, 2013

Organized Chaos Makes the Beauty of a Butterfly

Butterfly wing

Butterfly wing via squinza

This is a lesson about uncertainty.

A butterfly’s colors come from its scales, each a single cell, pigmented a single hue.

At pattern boundaries, scales of different colors intermingle. Transitions and shading are achieved by varying the proportions of the mix. It’s beautiful. It is also, in the language of molecular biology, a model for a stochastic mechanism of gene expression.

Each scale’s fate is not preordained. For example, cells on the surface of a swallowtail’s wings were not originally specialized to be yellow or blue or black. Instead, they contain genes potentially capable of producing each of those pigments.

What determines the color of each butterfly scale is, in a word, chance.

A molecule hits a piece of cellular machinery at just the right moment, in just the right place, and a gene produces a certain pigment. There’s no guarantee it will happen. It’s a matter of probability and moment-to-moment randomness. (The same probabilistic mechanism underlies the portions of the wings with solid colors, too. In those parts, molecules that trigger genes for one color are present at such high concentrations that the final color outcome is assured.)

In biology, there’s a tendency to conceive of randomness as noise, an accidental factor, a product of error—random genetic mutations, For example, random genetic mutations are mistakes in a chromosome-duplicating system that’s supposed to make perfect copies. Random mutations might be harmful, or insignificant, or beneficial, but they’re fundamentally mistakes, a disorderly deviation from an orderly system.

What makes a butterfly’s wings so remarkable isn’t just that unpredictabilities underlie their colors, but that they’ve harnessed the probabilities 1.

Randomness and uncertainty are translated into the ordered, functional patterns of a monarch or checkerspot. And in this, the butterfly’s wing is not unique, but a manifestation of principles ubiquitous in biology.

Let’s put on our Powers of Ten goggles and increase our magnification to where cell activity occurs, the level of so-called cellular machinery.

We’ll have to abandon that metaphor, though: Cells indeed contain complicated, task-performing structures, but the word “machine” is a product of the macroscopic world. We think of machines as rigidly assembled, with predefined purposes. At the cellular level, the analogy falls apart.

Out at the leading edges of theoretical and computational and experimental biology, where known and unknown meet, cellular machines have been redefined 2. The proteins of which they’re made don’t fold and unfold and operate according to some stepwise blueprints. Shape and function are exquisitely sensitive to infinitesimal energetic shifts, to the motion of atoms and the forces they exert.

Rather than a cellular factory, imagine a restaurant with a kitchen where blenders turn into convection ovens and whisks into knives when someone walks by, raising ambient temperatures by a fractional degree.

Imagine that the whole kitchen is like this, that cooks and prep staff, though they move with intent, can’t help but wander around—and still the 7-course meals come rolling through the doors.

Undoubtedly this metaphor has its own problems, but it gets the point across: The cellular world is an ever-fluctuating place. It’s full of randomness and, when things aren’t narrowly random, with uncertainty. Atoms and molecules and gradients change from moment to moment, and proteins with them.

Butterfly wing 2
Butterfly image via rougenair

Here one might ask where uncertainty comes from: Is it truly uncertain?

Might every molecular fate be predicted, if only we knew the motions and properties of every particle in a cell?

Or does quantum physics enter the equation at some level, with all its spooky uncertainties and strange probabilities shaping biology in some fundamental way?

That we don’t know, and might never. It’s a question too hard to study. Whatever the case, certain molecular activities are, best as we can describe them, random or probabilistic.

And we know, up at the cellular level, that a cell’s fate—whether an embryonic stem cell becomes specialized for service in kidney or liver, whether a blood stem cell grows up to carry oxygen or identify pathogens—is to some extent stochastic, determined by a signal that may or may not appear.

What’s extraordinary is that from all this uncertainty, form arises. Two identical twins, after trillions upon trillions of cell divisions, actually look the same to our eyes.

Out of disorder/order, though having identical genomes,is no guarantee of identical outcomes. Indeed, stochastic role in cells became evident when genetically matched yeast colonies, raised in the exact same environments, developed in very different ways.

What seems to explain that is variation in so-called epigenetic responses—processes that alter gene activity according to environment and circumstance, allowing organisms to change their biology in response to life’s unpredictable demands.

The different yeast colonies had different epigenetics and they responded to uncertainty differently. That might itself have been the product of chance, some “inherited stochastic variation,” though the benefits are obvious.

It’s evolutionary bet-hedging, a way of increasing the adaptive possibilities for one’s descendants, despite their genetic similarities.

Again, we see biology using uncertainty, building on it, making it integral to life. And it’s evident not only in epigenomes, but in genomes: When we look at our own, which for each of us contain some number of apparently random errors produced by copy-making glitches, we find that the errors are not randomly distributed. Mutations occur at different rates in different parts of the genome.

This isn’t the same thing as saying that certain sequences tend to stick around over evolutionary time, because errors there are more likely to cause problems. Instead, the potential for a random error to occur in the first place fluctuates across the genome. At every cellular level, randomness is harnessed.

Life is a study in contrasts between randomness and determinism,” wrote biochemists Arjun Raj and Alexander van Oudenaarden in an article entitled, “Nature, Nurture or Chance,” in the journal Cell. “From the chaos of biomolecular interactions to the precise coordination of development, living organisms are able to resolve these two seemingly contradictory aspects of their internal workings.”

Do these resolutions occur at even higher levels? Pattern from chance in populations, species, communities, ecology?

And in our own lives?

We can’t look at societies or lives the way we do cells, but certainly we feel it, at some intuitive level. “I think back on the trajectory of my life, and I think: I happened to bump into this person on the train, and it led to this or that,” Raj told me. “So many things are unpredictable on a long time scale, though it feels like they are predictable in the moment.”

I think on my own life: My parents met on a train. My closest friends came from chance encounters in a subway station, a class, a hockey team, a writing assignment. I can’t imagine my life without them, yet each of those meetings was profoundly, unsettlingly improbable.

And why stop with friendships? Why not scale up to the level of the universe itself, where order and disorder interpolate in random patterns?

There, perhaps, from the perspective of God or some alien cosmologist or deep time or whatever you use to imagine inconceivable vastness, we might find order yet again. Who knows for certain; we likely never will. But we can look at a butterfly’s wing and wonder.

(1) The pigment-synthesizing genes that guide coloration in a butterfly’s wing are an ideal model system because they’re relatively simple and straightforward. That’s the exception, not the rule.

Most traits involve multi-layered cellular and genetic relationships: networks of interactions nestled inside networks of interactions, often behaving in nonlinear ways, a whole biological nesting doll of complication. Which makes their harnessing of randomness and uncertainty all the more extraordinary.

(2) There’s a certain amount of uncertainty to these descriptions. It’s fairer to say, some scientists who study these matters think this is happening, and the fragments of biochemical data we’re able to retrieve at molecular and atomic scales inside cells match our computational models, but it’s slow going.

Take, for example, the modeling of protein folding and unfolding described in this PNAS article, produced by a custom-designed, massively parallel piece of dedicated hardware that’s roughly 100 times more powerful than any other machine used for this purpose. Running at full power over the course of a day, it can model a scant 10 microseconds of molecular cell dynamics. Run it for 2,737 years, and you’d describe one second.

Brandon Keim (@9brandon) is a freelance journalist specializing in science, environment, and culture. Based in Brooklyn and Bangor, Maine, he often carries sidewalk caterpillars to safety.

Famine Hecatomb in Lebanon (1915-18)

Lebanon had a calamitous decade (1909-1918).

In 1909, waves of deadly diseases such as typhus, cholera, diphtheria… swept the cities and towns in current coastal Lebanon and in Mount Lebanon.

Many Lebanese, particularly Christians, immigrated. Their preferred destination was the USA and Egypt, but the ship captains would on many occasion drop the people in Africa and Latin America and telling them: “This is America

Linda Schatkowski Schilcher dissected the German and Austrian sources and achieves for her book “The Famine of 1915-18 in Greater Syria” and advanced the number of 500,000 victims of famine and related to famine in Syria and Lebanon, 200,000 of them died in Mount Lebanon, particularly in the districts of Byblos and Betroun and Tripoli.

For example, the village of Abdilleh lost 35% of its people and the town of Chabtine 63%.

How people die of Starvation?

“Due to absolute lack and bad quality of food, people experienced terrible feet swelling, and many fell exhausted on the roads, vomiting blood… The dead toddlers and kids were thrown with the garbage in the corners of the villages. Chariots collected them and dumped them in public ditches. These horror spectacles were observed in the villages of Bilad Jubeil and Bilad Batroun and the city of Tripoli…”

The Turkish feminist author Halide Edib wrote in her Memoirs: “The nights in Beirut were atrocious: You heard the whining and screaming of starved people “Ju3an, Ju3an” (I’m hungry, I’m famished)

Jubran Khalil Jubran wrote to Mary Haskell:

“The famine in Mount Lebanon has been planned and instigated by the Turkish government. Already 80,000 have succumbed to starvation, and thousands are dying every single day. The same process happened with the Christian Armenians and applied to the Christians in Mount Lebanon…”

What were the main causes for this endemic famine?

1. Turkey had joined Germany in WWI on November of 1914, and France landed in a few Islands on the coast such as Arwad, and established a maritime blockade that secured that no foodstuff reach Lebanon and Syria.

2. General Jamal Pasha instituted an internal blockade of cereals to enter Mount Lebanon, particularly the Christian Maronite Canton (Kaemmakam) that included the current districts of Kesrowan and Betroun. Consequently, the Lebanese could not receive wheat and cereals from the district of Akkar and the Bekaa Valley.

Mind you that the people in Mount Lebanon relied on the grains from Akkar and the Bekaa for immediate need, but relied on the grain arriving from Syria for the winter reserves.

3. In April of 1915, the locusts ate the green and the dry (akhdar wa yabess) of the harvests and plants for 3 months.

4. The Turkish troops had already emptied the grain reserves of the Lebanese homes at the start of the war, and there were no ways to replenish any foodstuff.

5. The war lasted 4 years, but the Lebanese suffered an extra year of famine: 10,000 kids were roaming the roads at the end of 1918, begging for crumbs of bread

Famished people from the coastal towns thought that they might get some relief in the higher altitude regions (Jroud of Bilad Jubail and Bilad Betroun) and they died there. In a single town, over 3,800 of them were buried in a communal ditch because the town refused to bury them close to the churches of the town.

Najib Murad-Diyarbakri mentioned in his book “Sinine al Ghala” (Years of expensive prices) a Lebanese epitaph that read as a poem:

“They died from famine along the roads,

No father or mother or anyone to pity on them

We witnessed couples perishing from the cold

In this rough climate…

And not receiving absolution from a priest or anybody

The Drums of war are beating their sad rhythm

And the living people, wrapped in their shroud

Believing the war will not last a year…

Dear God, may this fifth year be the end of it”

Even in 1933, Charles Corm noted: “In a single afternoon, I counted 823 houses without roofs, doors and windows between Kesrowan and Betroun…”

Note 1: Even in August 7, 1914, the Jesuit priest Joseph Delore urged the Catholic Missions in “Immense material and morale distress in Lebanon” to quickly come to the rescue.

Note 2: Stories are still being circulated in my hometown of Beit-Chabab (Metn district) that a few amassed wealth during the war by hoarding properties in exchange of a loaf of bread. The contraband from Syria was in full swing, and those with connections reaped wealth from the miseries of the little hapless people…

Note 3: Official Lebanon is doping its hardest to bury this famine calamity, on the ground that it is a shame to mention people dying of hunger.  Instead, Official Lebanon celebrate the hanging of 6 Lebanese by Jamal Pasha as martyrs.

Note 4: A decade ago, I knew a wonderful elderly couple in Montgomery County, originally from Adbelli, and they were in fine physical health. Jean was recounting how the people in the town were expecting to see the bed sheet displayed in the morning, as they got married in the town. Elizabeth would have nothing of that nonsense, and the sheet was never displayed from the window to show any red blotches.

Note 5: The locust came on whatever was still edible after the Turkish army grabbed the harvest for its war front on the Suez Canal

Confessions Of A Syrian Activist: “I Want Assad To Win”

To one prominent activist, Syria’s revolution is already lost.

“If we keep going down this line, I think this will be known in history as the Islamic revolution in Syria.”

This Syrian activist got engaged into Syria’s revolution from its early days. He organized protests, documented the deadly crackdowns and disseminated the news, risking his life. And this interview was conducted in ANTAKYA, Turkey.

When the opposition took up arms, he worked closely with rebel groups, helping to spread their message of resistance and taking toll of the war’s carnage in places journalists couldn’t reach.

He has won widespread recognition for his work, and he remains deeply involved in the struggle today — though he no longer calls it a revolution. In fact, he thinks it needs to end.

BuzzFeed Staff Mike Giglio posted this Nov. 12, 2013

The activist works under his real name, but he requested anonymity to give the candid assessment of the conflict laid out in these remarks, which are compiled from a recent in-depth interview.

Asked to speak on the record, he deliberated with friends and colleagues and ultimately declined. He says he fears a backlash: His words could be used to undermine his work, or he could be misunderstood. He also cites safety concerns. But he believes that his message, unpopular among his revolutionary colleagues, is one they need to hear that:

1. Their revolution has ended;

2. A dangerous wave of Islamic extremism has welled up in its place; that

3. The insurgents should work to stop the fighting now; and that

4. If they can’t, they should hope it’s Syrian President Bashar al-Assad who wins.

“To simply say I want Assad to win would be a disaster if anyone heard it. But we’ve created a monster. For too long on the ground, there was too much focus on the crimes the regime was committing and not enough on our own problems. And addressing these problems was always being delayed.

“So we knew there was some sort of Islamism in the fighting, even when it was starting back in 2012 and we would ignore this, because we would say it would all end soon — Assad is going to fall in two weeks; Assad is going to fall in a month; Assad’s going to fall in Aleppo.

At each moment, we thought it was going to end very soon, and that meant we were neglecting the mistakes that we have been making [among the revolution]. We were thinking, OK, the regime’s going to fall, and we can solve this later. We just need to get rid of Assad. This was a big mistake.

“To that extent, we’ve created ISIS [the Islamic State in Iraq and Syria, a powerful al-Qaeda affiliate that is gaining ground in the rebellion]. And we’ve created Jabhat al-Nusra [another Qaeda-linked group].”

The activist has little hope for a political solution — a peace conference expected in Geneva this month was delayed again this week. Even if talks moved ahead, he adds, the moderate opposition wouldn’t have much say.

“We’ve reached this point where we have two powers that are recognized by the international community — the Syrian regime and the extremist groups on the ground. The third group [the moderate opposition] is very weak, even though it’s the majority in Syria. We don’t have anyone to defend the group. We don’t have weapons. We don’t have finances. We don’t have media.

“So yes, if I’m going to choose which side I wish would win at this stage, I would choose the side that’s already in power rather than seeing the extremist side jump into power and destroy everyone else.

The extremist groups do not seek a revolution in Syria — or at least, not a democratic one. They seek an Islamic one. And it’s something that’s not accepted by the majority of the country, whether you support Assad or you don’t. I would prefer that Assad wins at a stage like this for one reason: all of the other alternatives are totally unacceptable.

“I would not cheer the idea of Assad winning. I would not help in any way. But I will accept it. Adding that he’d keep up his fight against the government

“I have no guarantees to offer in government-controlled areas that if those areas are ‘liberated,’ we can keep you safe. That it will not be ISIS and Jabhat al-Nusra in charge, and that you won’t live under their laws. If I could make that guarantee, then I would support the idea of bringing down the regime without a political solution.”

The Islamic extremists threatening to overtake the rebellion pose more of a threat than Assad. “There is no language between civil society and Islamic authority in Syria right now. There’s no dialogue. It’s unacceptable”.

“In the same way,  if you say anything about Assad you’re doomed, if you say anything about God, you’re also doomed. It’s the same way of reacting, but the Islamic system is a much more lethal system, because it depends on an ideology that says, ‘God, who is the creator of the universe, says that we’re in charge. And if you stand against that, then you stand against the creator of the universe. And we will chop your heads off, chop your hands off. We will whip you. We will prevent you from speaking out.’ I think the ability of this Islamic authority and these extremist groups to abuse the citizens of Syria is much higher than that of the Syrian regime.

“A lot of people would argue that, if the regime wins, there would be no space whatsoever for another revolution, because the regime would come back 10 times stronger. The majority of people say that. I think that’s total nonsense.

The activist says that the moderate opposition is much more capable of resisting Assad than it was before the revolution, when political life was stifled and activists worked in the shadows, often unknown even to each other.

What we have in Syria now is local councils,” the activist says, referring to the civilian administrative groups that have sprouted up in rebel-held territory across the country, “and political and activist groups, whereas before March 2011 we had nothing. It was just a few people that were anonymous online.

“We have groups now. We have experience. We know how to perform demonstrations now. We know how to have contact with the media. We know how to provide aid and how to set up field hospitals. It’s a totally different situation now. And we learned from our mistakes.

“I think it’s definitely possible to see a revolution in the future. But if we don’t accept that we have lost now—that our revolution has stopped, or been put on pause, and that is a big dispute among activists—then that means that everything that’s happening now, and all the crimes that are being committed by Jabhat al-Nusra and ISIS, will be written in history as part of the Syrian revolution.

Do you see what I mean? If we can differentiate between this period that was the Syrian revolution, and this period now that is a messy situation that came as a result of a dictator standing against a revolution, then I think we can keep our revolution clean and our aspirations clean and our ideals in place. But if we keep going down this line, then we will turn our revolution into an Islamic revolution, and I think this will be known in history as the Islamic revolution in Syria.

“I’m not going to be able to say things like this publicly—because it would be misunderstood and misinterpreted, in a very messy situation in Syria where now it’s easy for you to be accused of being an agent for the West or an agent for the government. It’s very easy for people to point fingers and accuse you of working against the Syrian revolution. I worry about being misinterpreted or misunderstood and not being able to remain a player on Syria. I’m involved, and I have some sort of effect. I want to continue to be able to do that.

“It’s really about being responsible and saying, ‘OK, 100,000 people have been killed. Do we want another 100,000 to be killed?’ Maybe another 100,000 would be killed anyway. But do we want them to die for the exact reason that we were stubborn? And that’s the question.

Note 1: Chapeau bas. I agree with this lucid reasoning. I think that many wanted the regime to step aside in the beginning, and the turn of events gave the regime a breath of political validity.  That Bashar Assad is in a better position to deliver on meaningful reforms, as long as the moderate opposition keeps the pressures, internally and externally.

Note 2: Behind Geneva 2 https://adonis49.wordpress.com/2013/11/08/behind-the-frantic-activities-for-a-syrian-peaceful-transition-in-geneva-2-conference-this-human-disastrous-calamity-and/


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