A Momentary Flow

Updating Worldviews one World at a time

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61 posts tagged Life

Life doesn’t make trash - A genome is not a blueprint for building a human being, so is there any way to judge whether DNA is junk or not? - Humans are astounding creatures, our unique and highly complex traits encoded by our genome – a vast sequence of DNA ‘letters’ (called nucleotides) directing the building and maintenance of the body and brain. Yet science has served up the confounding paradox that the bulk of our genome appears to be dead wood, biologically inert junk. Could all this mysterious ‘dark matter’ in our genome really be non-functional? Our genome has more than 20,000 genes, relatively stable stretches of DNA transmitted largely unchanged between generations. These genes contain recipes for molecules, especially proteins, that are the main building blocks and molecular machines of our bodies. Yet DNA that codes for such known structures accounts for just over 3 per cent of our genome. What about the other 97 per cent? With the publication of the first draft of the human genome in 2001, that shadow world came into focus. It emerged that roughly half our DNA consisted of ‘repeats’, long stretches of letters sometimes found in millions of copies at seemingly random places throughout the genome. Were all these repeats just junk? To answer this question, hundreds of scientists worldwide joined a massive science project called the Encyclopedia of DNA Elements, or ENCODE. After working hard for almost a decade, in 2012 ENCODE came to a surprising conclusion: rather than being composed mostly of useless junk, 80 per cent of the human genome is in fact functional. (via Is our genome full of junk DNA? – Itai Yanai and Martin Lercher – Aeon)

Life doesn’t make trash
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A genome is not a blueprint for building a human being, so is there any way to judge whether DNA is junk or not?
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Humans are astounding creatures, our unique and highly complex traits encoded by our genome – a vast sequence of DNA ‘letters’ (called nucleotides) directing the building and maintenance of the body and brain. Yet science has served up the confounding paradox that the bulk of our genome appears to be dead wood, biologically inert junk. Could all this mysterious ‘dark matter’ in our genome really be non-functional? Our genome has more than 20,000 genes, relatively stable stretches of DNA transmitted largely unchanged between generations. These genes contain recipes for molecules, especially proteins, that are the main building blocks and molecular machines of our bodies. Yet DNA that codes for such known structures accounts for just over 3 per cent of our genome. What about the other 97 per cent? With the publication of the first draft of the human genome in 2001, that shadow world came into focus. It emerged that roughly half our DNA consisted of ‘repeats’, long stretches of letters sometimes found in millions of copies at seemingly random places throughout the genome. Were all these repeats just junk? To answer this question, hundreds of scientists worldwide joined a massive science project called the Encyclopedia of DNA Elements, or ENCODE. After working hard for almost a decade, in 2012 ENCODE came to a surprising conclusion: rather than being composed mostly of useless junk, 80 per cent of the human genome is in fact functional. (via Is our genome full of junk DNA? – Itai Yanai and Martin Lercher – Aeon)

Flowchart: David Foster Wallace On How To Live A Compassionate Life - In “This Is Water,” David Foster Wallace offers thoughts on living a compassionate life. Jessica Hagy beautifully illustrates them here. - If you’re automatically sure that you know what reality is, and you are operating on your default setting, then you, like me, probably won’t consider possibilities that aren’t annoying and miserable … But if you really learn how to pay attention, then you will know there are other options. It will actually be within your power to experience a crowded, hot, slow, consumer-hell type situation as not only meaningful, but sacred, on fire with the same force that made the stars: love, fellowship, the mystical oneness of all things deep down. (via Flowchart: David Foster Wallace On How To Live A Compassionate Life | Co.Design | business design)

Flowchart: David Foster Wallace On How To Live A Compassionate Life
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In “This Is Water,” David Foster Wallace offers thoughts on living a compassionate life. Jessica Hagy beautifully illustrates them here.
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If you’re automatically sure that you know what reality is, and you are operating on your default setting, then you, like me, probably won’t consider possibilities that aren’t annoying and miserable … But if you really learn how to pay attention, then you will know there are other options. It will actually be within your power to experience a crowded, hot, slow, consumer-hell type situation as not only meaningful, but sacred, on fire with the same force that made the stars: love, fellowship, the mystical oneness of all things deep down. (via Flowchart: David Foster Wallace On How To Live A Compassionate Life | Co.Design | business design)

The search for life beyond Earth is on, but are we ready for what we’ll find?
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When we venture into space we don’t know what we’re looking for – unless it is ourselves
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We are the first generation of serious alien-hunters, according to planetary scientist Sara Seager of the Massachusetts Institute of Technology. “We are finally on the verge of being able to search for signs of life beyond our solar system around the nearest hundreds of stars,” Seager said this week – and she thinks we might find it in the next two decades. But are we ready for that? Astronomer Jocelyn Bell Burnell doesn’t think so. Like Seager, she anticipates “first contact” in the next 20 to 100 years, yet she recently declared us culturally unprepared. What, for one thing, will we say to them? Given the separation of space, and thus time – it takes more than four years for a radio signal to reach even the nearest star – we needn’t rush into a decision, though to my mind no one came up with a better suggestion than the eight-year-old son of one of Bell Burnell’s fellow panellists: “Please take me with you, and my friends, and all the penguins.” But the discovery of alien life is unlikely to lead to a conversation, not even one stilted by a decades-long time delay. The search for extraterrestrial intelligence (Seti), which scans the skies for messages encrypted in radio broadcasts and the like, has so far found not a whisper. Indeed, almost the only flurry of excitement came when Bell Burnell discovered pulsars in 1967: the regular lighthouse radio beam of these collapsed, rotating stars was initially suspected of being a purposeful signal. Seti has been rightly compared to the Victorian enthusiasm for spiritualism: an attempt to communicate with invisible simulacra of ourselves, in a quest motivated by cosmic loneliness. No, if we find aliens in our lifetime it most probably won’t be from their intentional messages but, as Seager explained, from inadvertent traces they leave in their planetary atmospheres. About 1,800 “exoplanets” (those that orbit other stars) have already been discovered. These numbers received a huge boost from the launch in 2009 of Nasa’s Kepler space observatory, but the James Webb space telescope, the successor of the Hubble, will take the search to a new level after its scheduled launch in 2018. (via The search for life beyond Earth is on, but are we ready for what we’ll find? | Philip Ball | Comment is free | The Guardian)

The search for life beyond Earth is on, but are we ready for what we’ll find?
-
When we venture into space we don’t know what we’re looking for – unless it is ourselves
-
We are the first generation of serious alien-hunters, according to planetary scientist Sara Seager of the Massachusetts Institute of Technology. “We are finally on the verge of being able to search for signs of life beyond our solar system around the nearest hundreds of stars,” Seager said this week – and she thinks we might find it in the next two decades. But are we ready for that? Astronomer Jocelyn Bell Burnell doesn’t think so. Like Seager, she anticipates “first contact” in the next 20 to 100 years, yet she recently declared us culturally unprepared. What, for one thing, will we say to them? Given the separation of space, and thus time – it takes more than four years for a radio signal to reach even the nearest star – we needn’t rush into a decision, though to my mind no one came up with a better suggestion than the eight-year-old son of one of Bell Burnell’s fellow panellists: “Please take me with you, and my friends, and all the penguins.” But the discovery of alien life is unlikely to lead to a conversation, not even one stilted by a decades-long time delay. The search for extraterrestrial intelligence (Seti), which scans the skies for messages encrypted in radio broadcasts and the like, has so far found not a whisper. Indeed, almost the only flurry of excitement came when Bell Burnell discovered pulsars in 1967: the regular lighthouse radio beam of these collapsed, rotating stars was initially suspected of being a purposeful signal. Seti has been rightly compared to the Victorian enthusiasm for spiritualism: an attempt to communicate with invisible simulacra of ourselves, in a quest motivated by cosmic loneliness. No, if we find aliens in our lifetime it most probably won’t be from their intentional messages but, as Seager explained, from inadvertent traces they leave in their planetary atmospheres. About 1,800 “exoplanets” (those that orbit other stars) have already been discovered. These numbers received a huge boost from the launch in 2009 of Nasa’s Kepler space observatory, but the James Webb space telescope, the successor of the Hubble, will take the search to a new level after its scheduled launch in 2018. (via The search for life beyond Earth is on, but are we ready for what we’ll find? | Philip Ball | Comment is free | The Guardian)

Evolution depends on rare chance events, ‘molecular time travel’ experiments show - Chance events may profoundly shape history. What if Franz Ferdinand’s driver had not taken a wrong turn, bringing the Duke face to face with his assassin? Would World War I still have been fought? Would Hitler have risen to power decades later? Historians can only speculate on what might have been, but a team of evolutionary biologists studying ancient proteins has turned speculation into experiment. They resurrected an ancient ancestor of an important human protein as it existed hundreds of millions of years ago and then used biochemical methods to generate and characterize a huge number of alternative histories that could have ensued from that ancient starting point. Tracing these alternative evolutionary paths, the researchers discovered that the protein – the cellular receptor for the stress hormone cortisol – could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These “permissive” mutations had no effect on the protein’s function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein’s modern-day form to evolve. The researchers describe their findings June 16, online in Nature. “This very important protein exists only because of a twist of fate,” said study senior author Joe Thornton, PhD, professor of ecology & evolution and human genetics at the University of Chicago. “If our results are general – and we think they probably are – then many of our body’s systems work as they do because of very unlikely chance events that happened in our deep evolutionary past,” he added. Thornton specializes in ancestral protein reconstruction, a technique that uses gene sequencing and computational methods to travel backwards through the evolutionary tree and infer the likely sequences of proteins as they existed in the deep past. Through biochemical methods, these ancient proteins can be synthesized and introduced into living organisms to study their function. Thornton and others have previously shown that the evolution of modern-day proteins required permissive mutations in the past. But no one had ever investigated whether there were many or few other possible permissive mutations that could have happened, so it remained unknown how unlikely it is that evolution discovered a permissive pathway to the modern function. (via Evolution depends on rare chance events, ‘molecular time travel’ experiments show)

Evolution depends on rare chance events, ‘molecular time travel’ experiments show
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Chance events may profoundly shape history. What if Franz Ferdinand’s driver had not taken a wrong turn, bringing the Duke face to face with his assassin? Would World War I still have been fought? Would Hitler have risen to power decades later? Historians can only speculate on what might have been, but a team of evolutionary biologists studying ancient proteins has turned speculation into experiment. They resurrected an ancient ancestor of an important human protein as it existed hundreds of millions of years ago and then used biochemical methods to generate and characterize a huge number of alternative histories that could have ensued from that ancient starting point. Tracing these alternative evolutionary paths, the researchers discovered that the protein – the cellular receptor for the stress hormone cortisol – could not have evolved its modern-day function unless two extremely unlikely mutations happened to evolve first. These “permissive” mutations had no effect on the protein’s function, but without them the protein could not tolerate the later mutations that caused it to evolve its sensitivity to cortisol. In screening thousands of alternative histories, the researchers found no alternative permissive mutations that could have allowed the protein’s modern-day form to evolve. The researchers describe their findings June 16, online in Nature. “This very important protein exists only because of a twist of fate,” said study senior author Joe Thornton, PhD, professor of ecology & evolution and human genetics at the University of Chicago. “If our results are general – and we think they probably are – then many of our body’s systems work as they do because of very unlikely chance events that happened in our deep evolutionary past,” he added. Thornton specializes in ancestral protein reconstruction, a technique that uses gene sequencing and computational methods to travel backwards through the evolutionary tree and infer the likely sequences of proteins as they existed in the deep past. Through biochemical methods, these ancient proteins can be synthesized and introduced into living organisms to study their function. Thornton and others have previously shown that the evolution of modern-day proteins required permissive mutations in the past. But no one had ever investigated whether there were many or few other possible permissive mutations that could have happened, so it remained unknown how unlikely it is that evolution discovered a permissive pathway to the modern function. (via Evolution depends on rare chance events, ‘molecular time travel’ experiments show)

Life Magnified: The Alien Familiarity of the Cellular World
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A new collection from the National Institutes of Health offers a zoomed-in perspective of the world.
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Our universe is a vast and repeating tapestry of convergences. This how we experience it anyway, and in part because our brains are hardwired to recognize patterns. We can’t help but see the fractal echo of tributaries in a blown-up image of our own capillaries. And it makes sense that a network of Earth’s waterways might resemble a system of human blood vessels; it’s just not the sort of observation that most vantage points allow. Looking at something familiar from an unfamiliar perspective—often from very far away or from very close up—can be revealing this way. Such perspectives abound in science, where microscopes and telescopes allow us to access new worlds over extreme distances and through painstaking repetition. You can catch a glimpse of this world in a new exhibit curated by the National Institutes of Health called Life: Magnified, which includes remarkable scientific images—many come from NIH-backed projects—including a striking forest of gecko toe hair, the sunflower burst of a human liver cell, the fine spiderwebbing that creeps up blood vessel walls, and stunning solar systems of cells. The American Society for Cell Biology’s director calls it a “dazzling trip through the cellular world, which is both foreign and as close as [your] own skin.” (via Life Magnified: The Alien Familiarity of the Cellular World - Adrienne LaFrance - The Atlantic)

Source The Atlantic

Milky Way may have 100 million life-giving planets
“It seems highly unlikely that we are alone.” 
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There are some 100 million other places in the Milky Way galaxy that could support life above the microbial level, reports a group of astronomers in the journal Challenges (open access), based on a new computation method to examine data from planets orbiting other stars in the universe. “This study does not indicate that complex life exists on that many planets; we’re saying that there are planetary conditions that could support it, according to the paper’s authors*. “Complex life doesn’t mean intelligent life — though it doesn’t rule it out or even animal life — but simply that organisms larger and more complex than microbes could exist in a number of different forms,” the researchers explain. The scientists surveyed more than 1,000 planets and used a formula that considers planet density, temperature, substrate (liquid, solid or gas), chemistry, distance from its central star and age. From this information, they developed and computed the Biological Complexity Index (BCI). The BCI calculation revealed that 1 to 2 percent of the planets showed a BCI rating higher than Europa, a moon of Jupiter thought to have a subsurface global ocean that may harbor forms of life. With about 10 billion stars in the Milky Way galaxy, the BCI yields 100 million plausible planets. The authors cite one study that suggests that “some exoplanets may be more optimally suited for life than Earth. … Such ‘superhabitable’ worlds would likely be larger, warmer, and older, orbiting dwarf stars.” “It seems highly unlikely that we are alone,” say the researchers. “We are likely so far away from life at our level of complexity that a meeting with such alien forms might be improbable for the foreseeable future.” (via Milky Way may have 100 million life-giving planets | KurzweilAI)

Milky Way may have 100 million life-giving planets
“It seems highly unlikely that we are alone.”
-
There are some 100 million other places in the Milky Way galaxy that could support life above the microbial level, reports a group of astronomers in the journal Challenges (open access), based on a new computation method to examine data from planets orbiting other stars in the universe. “This study does not indicate that complex life exists on that many planets; we’re saying that there are planetary conditions that could support it, according to the paper’s authors*. “Complex life doesn’t mean intelligent life — though it doesn’t rule it out or even animal life — but simply that organisms larger and more complex than microbes could exist in a number of different forms,” the researchers explain. The scientists surveyed more than 1,000 planets and used a formula that considers planet density, temperature, substrate (liquid, solid or gas), chemistry, distance from its central star and age. From this information, they developed and computed the Biological Complexity Index (BCI). The BCI calculation revealed that 1 to 2 percent of the planets showed a BCI rating higher than Europa, a moon of Jupiter thought to have a subsurface global ocean that may harbor forms of life. With about 10 billion stars in the Milky Way galaxy, the BCI yields 100 million plausible planets. The authors cite one study that suggests that “some exoplanets may be more optimally suited for life than Earth. … Such ‘superhabitable’ worlds would likely be larger, warmer, and older, orbiting dwarf stars.” “It seems highly unlikely that we are alone,” say the researchers. “We are likely so far away from life at our level of complexity that a meeting with such alien forms might be improbable for the foreseeable future.” (via Milky Way may have 100 million life-giving planets | KurzweilAI)

We started by saying that what discriminates living from non-living systems is a sense of purpose. If biology is reducible to quantum physics, and typical quantum objects such as atoms and molecules show no sense of purpose, where does the transition occur? Where does the ‘desire’ to achieve the state of kinetic stability come from? This, of course, brings us back to square one. One easy way out is to conclude that purposefulness is simply an illusion. Pross would probably say that it is an emergent property that arises when chemistry becomes complicated enough. But given that this sense of purposefulness is how we identify life in the first place, perhaps we should resist conclusions that seem to wave it away too easily.

Vlatko Vedral – Evolution equation

It is no accident that the first person to talk qualitatively about life within the confines of the Second Law was also Boltzmann. Here is what he said: ‘The general struggle for existence of animate beings is not a struggle for raw materials — these, for organisms, are air, water and soil, all abundantly available — nor for energy, which exists in plenty in any body in the form of heat, but a struggle for [negative] entropy, which becomes available through the transition of energy from the hot sun to the cold earth.’ For Boltzmann, life is trying to stay away from equilibrium, away from the state of inanimate (dead) matter. It does this by sucking in low-entropy stuff from the environment, thereby pushing its own levels of disorder away from the maximum. Another pioneer of quantum physics, the Austrian physicist Erwin Schrödinger, also emphasised the idea that life tries to maximise free energy, namely the energy available to do useful work. This is another way of saying that it wants to stay away from equilibrium. In this respect it differs from, for example, a stone, which when left to its own devices just stays as it is and does not try to do anything useful.

Vlatko Vedral – Evolution equation