A Treasure Trove of Undiscovered Life: Raw Sewage

By Rebecca Boyle

Bubbling Wastewater Kristian Bjornard/Wikimedia Commons

Raw sewage is apparently a gold mine for virologists in search of new quarry — it contains thousands of previously unknown virus species, according to a new study. Hopefully this unique finding will justify the nasty task of sifting through sewage for science.

Microbiologists at the University of Pittsburgh, Washington University in St. Louis and the University of Barcelona have been searching for novel ways to find new viruses. About 3,000 different viruses have been described so far, but this is probably a small fraction of the species that exist, the authors say. In a hunt for new examples, they explored sewage samples from sites in Africa, Europe and North America.

They used deep sequencing methods to explore viruses with various types of nucleic acids — single-stranded DNA, double-stranded DNA, positive-sense RNA and double-stranded RNA. This method of metagenomics, studying everything in an entire sample population, had been used before to study bacteria and viruses — but not from a a raw sewage sample.

The researchers found a few that they recognized, including human papillomavirus and norovirus, and a suite of plant and animal viruses. They also found bacteriophages, which makes sense because raw sewage also contains plenty of bacteria. In all, there were 234 known viruses from 26 distinct families — by itself, this makes raw sewage the most bountiful reserve of viruses ever found, according to a news release from Pitt.

But the vast majority of genetic sequences had little or no relation to known viruses, the researchers said. Most of them couldn’t even be placed into specific taxa.

“These results show that the vast majority of the viruses on Earth have not yet been characterized,” the authors write.

Uncovering new viruses will help microbiologists understand how viruses evolve and emerge, they added. Apparently raw sewage is a great place to look.

[ScienceDaily]

How To Spot Circulating Tumour Cells

Cancer cells that have broken away from the main tumour can spread the disease. Now scientists are developing better ways to find them

KFC 

One way that cancer spreads through the body is through circulating tumour cells. These are cancer cells that have broken away from the main tumour and begun to circulate in the blood. A new tumour can form if they become embedded elsewhere in the body and begin to grow.

So spotting circulating tumour cells is an important goal in the treatment of cancer.

Here's the problem though. Circulating tumour cells are extremely difficult to find. In a single millilitre of blood there are usually several billion red blood cells, several million white blood cells but fewer than ten circulating tumour cells.

And there is the only one way to find them. The cells can be made to look different from normal blood cells. So you need a highly trained cell biologist with a microscope and plenty of time. The words needle and haystack don't do this task justice.

Various groups are looking for better ways to find circulating tumour cells and their efforts fall essentially into two categories. The first is biochemical: trapping the cells using antibodies that bond to them. The second is mechanical: filtering them out.

Both of these methods have drawbacks. Antibodies can only bond to the cells if they can get close enough. And although circulating tumour cells are bigger than red blood cells, they are about the same size as white blood cells so filters have limited success..

Today, Markus Gusenbauer at St. Poelten University of Applied Sciences in Austria and a few buddies make some progress in this area. These guys have developed a computer model of the way blood flows through a bed of magnetic beads.

When a magnetic field is applied to such a bed, the beads line up into strings that together form a filter with a specific gap size. Whether a cell can pass through depends on its size and also its flexibility.

The Austrian team's model takes into account the size and flexibility of both red blood cells and circulating tumour cells to show how this kind of switchable filter could catch the bad guys.

The idea here is that the beads would also be covered in an antibody that latches onto the circulating tumour cells, keeping them trapped even when the magnetic field is switched off. This method uses both of the current techniques to overcome their drawbacks.

The plan would be to store the beads in a chamber in a microfluidic lab-on-a-chip device. A blood sample containing a handful of circulating tumour cells but billions of other types is pumped into the chamber and the magnetic field switched on.

This causes the beads to line up in a filter that traps the biggest cells. The antibodies on the beads then latch on to their targets, trapping them for later study.

That's the theory anyway. In reality, these guys have a lot more work to do before such a system can be made to work. For a start, circulating tumour cells come in a number of different flavours and the mechanical characteristics of each will need to be worked out.

More serious is the problem with white blood cells. Being a similar size to circulating cancer cells means they could easily clog these kinds of filters.

But the reality is that this kind of problem can only be solved by understanding what's going on on the level of individual cells and engineering a solution that works on this scale. That's why this kind of simulation is a useful first step.

Ref: arxiv.org/abs/1110.0995: A Tunable Cancer Cell Filter Using Magnetic Beads: Cellular And Fuid Dynamic Simulations

'I Loved What I Did'

Visionary: Apple chief executive Steve Jobs is silhouetted in the Apple logo at the Moscone Center in San Francisco, Monday, June 28, 2004.
AP Photo/Susan Ragan

COMPUTING

'I Loved What I Did'

What we can learn from the legacy and life of Steve Jobs.

• BY JASON PONTIN

Audio »

It's tolerably well known that newspapers and magazines bank the obituaries of the ailing famous. When Steve Jobs died last Wednesday, the encomia appeared with unsurprising haste. But I had nothing prepared. Ever since Jobs announced in 2004 that he had had surgery to remove a cancerous tumor from his pancreas, editors had urged me to get something down. (Only last week, an editor at Technology Review proposed that I might review Jobs's life as if it were a book or a tablet computer.) But I always demurred. It seemed ghoulish. Besides, I wanted Steve to live forever, because I loved him.

I had grown to love him even though our relationship (such as it was) had always been chilly. On at least two occasions, I know I pissed him off.

Steve Jobs was the first person I interviewed in Silicon Valley. It was 1994, and he was chief executive of NeXT Computer and exiled from Apple. The late Tom Quinlan, hardware editor ofInfoWorld, had given me a page of questions I did not understand, and, chuckling, dispatched me to NeXT's headquarters. It turned out to be a low, modernist building in Redwood City, down the road from Oracle's futuristic drums. The founder and CEO, when I met him, was intimidating and impatient. In a conference room that I can still remember was striped with shadows from the blinds on its windows, I peered at Quinlan's questions and nervously asked Jobs why he had no loyalty to his customers. (NeXT had just announced it would abandon its black-box computers and focus on developing software.) I think I asked why he made beautiful, expensive machines that only enthusiasts wanted. Jobs said, "Fuck you. I created the Mac and it's still the best. What have you done?" and was gone.

Well, he had a point, although I couldn't hear it at the time. Five years later, after he had returned to Apple, when I was editor of Red Herring, a magazine popular during the dot.com boom, I wrote a callow, facile column in the form of a letter to Jobs. It began, "Dear Steve, you've saved Apple. Good for you! I don't care." I argued that Microsoft had a near-monopoly in the market for personal computer software, and therefore controlled computing. Jobs wrote to my boss, Red Herring's chief executive, Tony Perkins: "I'll tell you who doesn't matter: Red Herring, so long as Jason is the editor." My final e-mail from Apple's founder, sent this July, was a terse two-word rejection ("No thanks!"). It seems a fitting terminus to our history.

But like millions on the planet, I felt I knew Jobs much better than I did. It was a natural delusion: I'd seen him on stage or on television many times, and I had studied the primary literature—the long, soul-baring 1985 interview in Playboy, for instance—and read the biographies and company histories. I knew the meters of his speech, how he would pause, without embarrassment, when answering a question that caught his searching intelligence. With the rest of the world, I watched him get old and sick. It was affecting to see a world-historical individual so nakedly human.

But, mostly, I loved Steve Jobs because of the products he created and the method by which he worked. The extraordinary success of his method and products made nonsense of the wised-up cynicism which Quinlan and I were peddling: Jobs made hundreds of millions of people into enthusiasts for Apple's personal technology. Today, the company enjoys near-monopolies in tablet computers and music players; and its iPhone outsells all other smart phones. Perhaps most surprisingly, sales of its computers have outpaced Windows PCs for years.

More than anyone else, Jobs shaped the forms of the machines of the digital revolution, and with those machines, the texture of modernity. He was responsible for six creations of unrivaled influence—successively, the Apple II, the Macintosh, the movie studio Pixar, the iPod, the iPhone, and the iPad—and they all bear the stamp of his obsessions and values. The products he oversaw were simple, elegant, and genuinely novel.

How did he do it? It's a paradox that has been endlessly worried over that Jobs's preoccupation with delighting consumers was accompanied by confidence that there was no point in asking what they wanted. A 1989 interview in Inc magazine contains the best account of his working method. After hedging that his process was "hard to explain," he offered up: "Customers can't anticipate what the technology can do. They won't ask for things that they think are impossible." But, he continued, "If it takes a long time to pull out of customers what they really want ..." it also "takes a long time to pull out of technology what it can really give." 

He elaborated:

"Sometimes the technology just doesn't want to show you what it can do. You have to keep pushing on it and asking the engineers over and over again to explain why we can't do this or that—until you truly understand it. A lot of times, something you ask for will add too much cost to the final product. Then an engineer might say casually, 'Well, it's too bad you want A, which costs $1,000, instead of B, which is kind of related to A. Because I can do B for just 50¢.' And B is just as good as A. It takes time to work through that process—to find breakthroughs but not wind up with a computer no one can afford."

In his obituaries, Jobs was called a visionary. The word is justified: he had visions, and he convinced cofounders, investors, employees, and, finally, customers to share them. Yet the word "visionary" suggests mysterious powers, and as the Inc interview shows, Jobs's approach wasn't so very strange. He pulled at consumers, and pushed at the technology, and merged the two. But if the method was not mysterious, the details were laborious. Jobs was not an engineer, and never wrote code, and so he was forced to work through others. He combined and refined borrowed ideas (from Xerox PARC most famously, but variously: from typesetters, industrial designers, and the counterculture). He ignored vulgar consensus, took risks, and killed unsatisfactory projects. He loved excellence; anything that was substandard, hurried, cluttered, or dumb pained him, and he rejected it. He concerned himself with the smallest details of products, so that, for example, the circuit board of the Apple II had to be flawlessly soldered and classically proportioned, though almost no one would ever see it. He hired the best designers and engineers, and by persuasion and bullying, inspired them to build his insanely great machines.  

Apple (and by extension Jobs) existed, he always said, at the intersection of the liberal arts and technology. As an artist, his medium of expression was computing. He wanted to excite passionate fandom from his customers, because he was himself technology's biggest fan. And like all real artists, he didn't create his artifacts to get rich (although the validation must have been nice to a poor boy from Mountain View); he did it for the absorbing love of his chosen craft.

During a justly famous speech at the 2005 Stanford University Commencement (the core text for understanding the man), Jobs spoke about getting fired from Apple. He said, "I was a very public failure, and I even thought about running away from the Valley. But something slowly began to dawn on me—I still loved what I did. The turn of events at Apple had not changed that one bit. I had been rejected, but I was still in love. And so I decided to start over."

Jobs insisted that getting fired from Apple was the best thing that could have happened to him: "The heaviness of being successful was replaced by the lightness of being a beginner again ... It freed me to enter one of the most creative periods of my life." During the next five years, he founded NeXT and Pixar and got married. NeXT led to his return to Apple, and he saw the technology he created at NeXT at the heart of the Macintosh operating system.

Jobs concluded:

"I'm pretty sure none of this would have happened if I hadn't been fired from Apple ... I'm convinced that the only thing that kept me going was that I loved what I did. You've got to find what you love. And that is as true for your work as it is for your lovers. Your work is going to fill a large part of your life, and the only way to be truly satisfied is to do what you believe is great work. And the only way to do great work is to love what you do."

Sad that he is dead, disappointed that I will never see the machines he might have created. I hope, in my small way, to imitate Steve.

Jason Pontin is the editor in chief of Technology Review.

Won Over

 

“Reaching that honored city, which was protected by the arms of the ten-headed Ravana, roaming about and not finding that highly respected daughter of King Janaka, who was won over by her husband’s divine qualities, that monkey then became highly distressed.” (Valmiki Ramayana, Sundara Kand, 7.16)

tataḥ sa tām kapir abhipatya pūjitām |
caran purīm daśa mukha bāhu pālitām |
adṛśya tām janaka sutām supūjitām |
suduhkhitām pati guṇa vega nirjitām ||

Those intimately associated with the Supreme Personality of Godhead substantiate their exalted position and remain steadfast to their occupational duty of being a lover of God not due to any outside obligation or social convention. The roles of brother, son, wife, father, mother, friend, and so on carry many responsibilities. It is said that “a friend in need is a friend indeed”, which means that a good friend is one who is around to help you through the bad times. Being a friend during times of peace is a lot easier than riding out the struggles with your good buddy who is in major distress. A real friend is always there for you, as they are attracted by your qualities and drawn to your association. With a wife, there is an inherent duty that she be there for the husband to support him. This is especially true when the marriage has been arranged by the parents and the couple married under religious principles. Lest we think that this was the main cause for Sita’s devotion to Rama, in the above referenced verse it is declared that she was drawn to Rama by His nature, won over by His divine qualities, orgunas. In this respect she became even more worthy of honor and worship from Shri Hanuman

 

, the faithful servant who had been tasked with finding her.

Sita’s glories actually know no end. To describe her only as the most beautiful woman in the world would be to shortchange her other qualities, which include kind-heartedness and benevolence. Anyone who is dedicated in thought, word and deed to the Supreme Lord can never be lacking in divine qualities. Scholars not of the bhakti attitude will try to compare Sita to characters from fictional literature and mythological traditions, but the search for anyone even similar to her will be a futile one. Sita is as real as the sun and her glories as everlasting as the infinite nature of time and space. Though she is endowed with every virtuous quality to an immeasurable extent, the devotees still try to describe some of her features and glorify her character, for this brings great joy to the heart. This joy is especially needed during times of distress, when success in a difficult task doesn’t seem certain.

When the couple was acting out their dramatic roles on this earth many thousands of years ago, one of the acts involved a period of separation. Lord Rama

 

 is a non-different form of the original Supreme Lord, who is known as Bhagavan in the Vedic tradition. Bhagavan is the most fortunate individual. In sports and areas of acclaim there is always the search for the greatest of all-time. Based on past performance and the ability to exercise skill, an individual will be labeled as being very great or better than anyone else to have ever done what they do. Lost in this mix, however, is the issue of fortune, or luck. Without good luck, without things going right for you more times than not, there is no question of success. In the grand scheme of things we are quite powerless, as the soul does not create actions nor is it responsible for the results of behavior. These are taken care of by nature, which is governed by the three modes of goodness, passion and ignorance, which operate under the purview of the Supreme Lord.

“Those with the vision of eternity can see that the soul is transcendental, eternal, and beyond the modes of nature. Despite contact with the material body, O Arjuna, the soul neither does anything nor is entangled.” (Lord Krishna, Bhagavad-gita, 13.32)

If we do see someone excel in a particular field, it is to be understood that they are fortunate. Their luck is good because they have been able to perform without impediment, without injury, and without loss of skill. They were also able to defeat their competitors, which means that the laws of nature did not place anyone in their way who could have defeated them. We may think we have control over our own actions, but we certainly can’t manage the behavior of others. Everything is placed into just the right circumstance to have the proper result always manifest.

God is described as Bhagavan because His fortune is higher than anyone else’s . He is the most beautiful, wise, strong, renounced, wealthy and famous. He is the reservoir of all pleasure and good fortune. When He appears on earth for whatever reason, these divine qualities come with Him. Therefore even when playing the role of the prince of the Raghu dynasty, Bhagavan retained His supreme standing.

Just as the original Personality of Godhead can descend to earth and maintain His stature, the Lord’s eternal consort also comes with Him. The distinguishing feature of the eternal consort is that she gives more pleasure to Bhagavan than anyone else. We could search the three worlds and every inch of space and never find anyone who gives more pleasure to Rama than Sita. She played the role perfectly of a devoted wife, married to Rama after a wonderful ceremony held in the kingdom of Videha ruled by King Janaka, Sita’s father.

Since Rama won Sita’s hand in marriage after lifting and breaking a powerful bow coming from Lord Shiva

 

, it would be understandable if Sita’s greatness would be attributed to her dedication to dharma, or virtue. In different fields of endeavor, there are specific guiding principles and recommendations to be followed. These help to maintain the ideal condition. With a marriage, the ideal condition is that the husband and wife live together peacefully and steadily advance in consciousness. Those who think of Bhagavan at the time of death immediately put an end to the cycle of birth and death known as samsara. Transmigration of the soul is a scientific concept that is mistakenly viewed to be a product of faith called reincarnation

 

.

Since the male species dominates the female, the duty applied to the wife is to be subservient to and supportive of her husband. This maintains the harmony within the marriage, as the male ego is very strong. Should the wife become predominant, the male ego gets bruised and problems arise. In reality, in most homes where happily married couples reside, the wife runs the show. It’s just that in good marriages the wife acts in such a way that the husband thinks that he is in charge. When both parties follow their prescribed duties, there is a better chance of advancing in consciousness.

Since Sita and Rama live forever in each other’s company, they don’t require adherence to dharma. In fact, they are the very objects of virtue and piety, as they are regularly remembered by those who follow bhagavata-dharma, or devotional service

 

. A set of guiding principles enables a specific condition to be reached, but since there can be no better condition than having God’s constant company, the set of principles belonging to bhagavata-dharma becomes the most inclusive and worthwhile to follow. Those who regularly chant, “Hare Krishna Hare Krishna, Krishna Krishna, Hare Hare, Hare Rama Hare Rama, Rama Rama, Hare Hare

 

”, can constantly remember Bhagavan and His eternal consort and the love they share for each other.

While on earth, Sita abided by her religious duties perfectly. Rama had a biological mother and two other mothers who were married to His father King Dasharatha. In this sense Sita inherited three mother-in-laws at the time of marriage. Yet she never failed to please any of them, honoring them as she would her own mother on a daily basis. More than anything, she was very chaste and wholly dedicated to Rama. This was done not out of duty necessarily, but more out of love for her husband. Rama’s divine qualities won Sita over, as they had previously done with Lakshmana

 

.

“I am His younger brother, Lakshmana by name. Due to His transcendental qualities, I have taken up service to Him, as He is grateful and very knowledgeable.” (Lakshmana speaking to Hanuman, Valmiki Ramayana

 

, Kishkindha Kand, 4.12)

Shri Lakshmana, Rama’s younger brother, was inseparable from Rama since childhood. Again, a younger brother’s duty as espoused by the Vedas is to worship the older brother and treat him like a father. In this respect Lakshmana was wholly deferent to dharma. But when he met Shri Hanuman, Lakshmana made sure to tell him that he was following Rama through thick and thin because of the Lord’s qualities. Twelve years after his marriage to Sita, Rama was ordered to leave the kingdom and not come back for fourteen years. Sita and Lakshmana insisted on accompanying Him, and while in the forest Sita would be kidnapped by a Rakshasa named Ravana. Rama and Lakshmana met up with Hanuman in Kishkindha after that.

Hanuman was the chief minister of the monkey-king Sugriva, so when he met Rama for the first time, there was also an underlying duty guiding his behavior. Sugriva tasked Hanuman with finding out what Rama and Lakshmana wanted, for their presence as fighters was conspicuous in a forest inhabited by animals and monkeys. Nevertheless, when Hanuman met Rama, he eventually forgot his initial purpose and instead became overwhelmed by the Lord’s brilliant qualities. Right then he decided that Rama was his object of worship and that he would dedicate his life to Him.

Jumping forward to when Hanuman was in Lanka searching for Sita, we see that he became dejected upon not finding her right away. Indeed, Hanuman saw everything there was to see in Lanka. The kingdom was extremely opulent, richer than any city seen today. Even the floors were inlaid with jewels and the buildings made of gold. Who could imagine such opulence? Though he appreciated this beauty, Hanuman was still dejected that he had yet to find Sita, who was the reason for his being in Lanka.

In the above referenced verse from the Ramayana it is said that Hanuman was dejected upon not having met the daughter of King Janaka. Amongst kings in the world at the time Janaka was one of the most respected. Initially well known for his mastery over mystic yoga, Janaka would later find a higher sensation by gaining Shri Rama as a son-in-law. Today Janaka is listed as one of the twelve authorities on devotional service. Therefore his daughter Sita would naturally be very exalted as well. It is also mentioned that Sita was well-worshiped. Though she was being held against her will in Lanka, she was the real precious gem in the city, not like the opulence that served as a façade to mask the dedication to the mode of ignorance of the residents. Despite their wealth, Ravana and the Rakshasas lived lives that were devoid of any meaning. Drinking wine and having illicit sex

 

 can only take you so far. When life is ruled by this behavior, it becomes empty very quickly. The soul is meant to pour out heaps of transcendental love. When there is no outlet for this love, perverse activities are adopted instead, leading to the opposite condition, wherein more misery and less happiness are encountered .

Sita had been conquered by the force of her husband’s qualities. Rama’s kindness, beauty, smiling face, and loving heart had won Sita over for life. In this sense her being drawn to Him represented another wonderful quality. Anyone who can say they have been subjugated by Bhagavan’s qualities can be considered highly fortunate. Many exalted saints and divine figures are also referred to as Bhagavan for this very reason. Rishi Narada knows no other business except glorifying Rama and spreading the nectar of His holy name across the world. Hence he is often referred to as Bhagavan, as is Lord Shiva, who is an expert on devotion to Rama, as he practices it as his primary business in life.

Sita’s wonderful qualities only increased Hanuman’s grief over not having found her. At the same time, the separation made him even more eager to search for her, through thick and thin, through both the good times and the bad. Ravana was very powerful, but he was not able to stop someone as devoted as Hanuman from finding the person who gives Rama more pleasure than anyone else. Just as Sita was won over by Rama’s qualities, Hanuman was eternally attached to Sita because of her level of devotion. In the same manner, the sincere souls hearing the tradition of the Ramayana and following the methods of worship instituted by the Vaishnava acharyas can’t help but be won over in the heart by Hanuman’s wonderful exhibition of devotion and dedication. One of Bhagavan’s many qualities is that He is unbeatable, or unconquerable. When the devoted soul makes their life’s mission the pleasing of Bhagavan, that same invincibility is passed on to them. Therefore Hanuman never had a chance of failing in his mission, and neither does anyone who is fortunate enough to hear about Rama’s most faithful servant on a regular basis.

In Closing:

The beloved daughter of Janaka in Lanka waits,

For her husband to rescue her from her dire straits.

Hanuman, from Kishkindha was sent,

Much time in Ravana’s land he spent.

Looking for Sita, to bring the news to her,

That Rama’s arrival in Lanka soon to occur.

But not finding that woman highly blessed,

Hanuman felt temporarily distressed.

Her qualities are second to none,

At pleasing Rama she is number one.

As wife devotion to husband from her everyone came to expect,

But more taken by Rama’s qualities was she, brilliant in every respect.

City of Lanka having opulence unimaginable,

Protected by arms of Ravana, strength formidable.

Without sight of princess, difficult for monkey to proceed,

But by remembering Sita, indeed would he succeed.