A Momentary Flow

Updating Worldviews one World at a time

Yet viewing our genome as an elegant and tidy blueprint for building humans misses a crucial fact: our genome does not exist to serve us humans at all. Instead, we exist to serve our genome, a collection of genes that have been surviving from time immemorial, skipping down the generations. These genes have evolved to build human ‘survival machines’, programmed as tools to make additional copies of the genes (by producing more humans who carry them in their genomes). From the cold-hearted view of biological reality, we exist only to ensure the survival of these travellers in our genomes.

Is our genome full of junk DNA? – Itai Yanai and Martin Lercher – Aeon
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)

I Contain Multitudes /Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing? / Your DNA is supposed to be your blueprint, your unique master code, identical in every one of your tens of trillions of cells. It is why you are you, indivisible and whole, consistent from tip to toe. But that’s really just a biological fairy tale. In reality, you are an assemblage of genetically distinctive cells, some of which have radically different operating instructions. This fact has only become clear in the last decade. Even though each of your cells supposedly contains a replica of the DNA in the fertilized egg that began your life, mutations, copying errors and editing mistakes began modifying that code as soon as your zygote self began to divide. In your adult body, your DNA is peppered by pinpoint mutations, riddled with repeated or rearranged or missing information, even lacking huge chromosome-sized chunks. Your data is hopelessly corrupt. Most genome scientists assume that this DNA diversity, called “somatic mutation” or “structural variation,” is bad. Mutations and other genetic changes can alter the function of the cell, usually for the worse. Disorderly DNA is a hallmark of cancers, and genomic variation can cause a suite of brain disorders and malformations. It makes sense: Cells working off garbled information probably don’t function very well. Most research to date has focused on how aberrant DNA drives disease, but even healthy bodies harbor genetic disorder. In the last few years, some researchers report that anywhere from 10 to 40 percent of brain cells and between 30 and 90 percent of human liver cells are aneuploid, meaning that one entire chromosome is either missing or duplicated. Copy number variations, in which chunks of DNA between 100 and a few million letters in length are multiplied or eliminated, also seem to be widespread in healthy people. (via Our Body as Genetic Patchwork: Helpful or Hurtful? | Simons Foundation)

I Contain Multitudes
/
Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing?
/
Your DNA is supposed to be your blueprint, your unique master code, identical in every one of your tens of trillions of cells. It is why you are you, indivisible and whole, consistent from tip to toe. But that’s really just a biological fairy tale. In reality, you are an assemblage of genetically distinctive cells, some of which have radically different operating instructions. This fact has only become clear in the last decade. Even though each of your cells supposedly contains a replica of the DNA in the fertilized egg that began your life, mutations, copying errors and editing mistakes began modifying that code as soon as your zygote self began to divide. In your adult body, your DNA is peppered by pinpoint mutations, riddled with repeated or rearranged or missing information, even lacking huge chromosome-sized chunks. Your data is hopelessly corrupt. Most genome scientists assume that this DNA diversity, called “somatic mutation” or “structural variation,” is bad. Mutations and other genetic changes can alter the function of the cell, usually for the worse. Disorderly DNA is a hallmark of cancers, and genomic variation can cause a suite of brain disorders and malformations. It makes sense: Cells working off garbled information probably don’t function very well. Most research to date has focused on how aberrant DNA drives disease, but even healthy bodies harbor genetic disorder. In the last few years, some researchers report that anywhere from 10 to 40 percent of brain cells and between 30 and 90 percent of human liver cells are aneuploid, meaning that one entire chromosome is either missing or duplicated. Copy number variations, in which chunks of DNA between 100 and a few million letters in length are multiplied or eliminated, also seem to be widespread in healthy people. (via Our Body as Genetic Patchwork: Helpful or Hurtful? | Simons Foundation)

Evolution and Entropy
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One of the surprising discoveries of Papadimitriou’s study is that natural selection values not just fitness, but also genetic diversity, which in more technical terms is referred to as entropy. This view that evolution optimizes not just mean fitness but mean fitness and entropy is not well known, “but I think it’s a deep observation,” Adami said. The Berkeley team isn’t the first to highlight the role entropy might play in evolution. But until now, the subject has mainly been of interest to mathematicians rather than biologists. “Applications of entropy in evolution have had a bad name, because they were very ill-defined,” Barton said. “More recently, there have been some interesting, and much sounder, ideas, which make a link between fields that are addressing a similar issue: Statistical physics and evolutionary biology both try to understand the overall properties of a complicated system, independent of the microscopic details.” These more recent results are mathematically sound, but they still don’t connect well with existing biological understanding, he said. “So it’s not clear to biologists how [the results] might help explain their open questions.”

Game Theory Makes New Predictions for Evolution | Simons Foundation
The Game Theory of Life
-Applying game theory to the behavior of genes provides a new view of natural selection. - In what appears to be the first study of its kind, computer scientists report that an algorithm discovered more than 50 years ago in game theory and now widely used in machine learning is mathematically identical to the equations used to describe the distribution of genes within a population of organisms. Researchers may be able to use the algorithm, which is surprisingly simple and powerful, to better understand how natural selection works and how populations maintain their genetic diversity. By viewing evolution as a repeated game, in which individual players, in this case genes, try to find a strategy that creates the fittest population, researchers found that evolution values both diversity and fitness. Some biologists say that the findings are too new and theoretical to be of use; researchers don’t yet know how to test the ideas in living organisms. Others say the surprising connection, published Monday in the advance online version of the Proceedings of the National Academy of Sciences, may help scientists understand a puzzling feature of natural selection: The fittest organisms don’t always wipe out their weaker competition. Indeed, as evidenced by the menagerie of life on Earth, genetic diversity reigns. “It’s a very different way to look at selection,” said Stephen Stearns, an evolutionary biologist at Yale University who was not involved in the study. “I always find radically different ways of looking at a problem interesting.” (via Game Theory Makes New Predictions for Evolution | Simons Foundation)

The Game Theory of Life

-Applying game theory to the behavior of genes provides a new view of natural selection.
-
In what appears to be the first study of its kind, computer scientists report that an algorithm discovered more than 50 years ago in game theory and now widely used in machine learning is mathematically identical to the equations used to describe the distribution of genes within a population of organisms. Researchers may be able to use the algorithm, which is surprisingly simple and powerful, to better understand how natural selection works and how populations maintain their genetic diversity. By viewing evolution as a repeated game, in which individual players, in this case genes, try to find a strategy that creates the fittest population, researchers found that evolution values both diversity and fitness. Some biologists say that the findings are too new and theoretical to be of use; researchers don’t yet know how to test the ideas in living organisms. Others say the surprising connection, published Monday in the advance online version of the Proceedings of the National Academy of Sciences, may help scientists understand a puzzling feature of natural selection: The fittest organisms don’t always wipe out their weaker competition. Indeed, as evidenced by the menagerie of life on Earth, genetic diversity reigns.
“It’s a very different way to look at selection,” said Stephen Stearns, an evolutionary biologist at Yale University who was not involved in the study. “I always find radically different ways of looking at a problem interesting.” (via Game Theory Makes New Predictions for Evolution | Simons Foundation)

Tigers need diverse gene pool to surviveStanford University Original Study
 New research shows that increasing genetic diversity among the 3,000 or so tigers left on the planet, though interbreeding and other methods, may be the key to their survival as a species. Iconic symbols of power and beauty, wild tigers may roam only in stories someday soon. Their historical range has been reduced by more than 90 percent. But conservation plans that focus only on increasing numbers and preserving distinct subspecies ignore genetic diversity, according to the study. In fact, following that approach, the tiger could vanish entirely. “Numbers don’t tell the entire story,” says Elizabeth Hadly, professor in environmental biology at Stanford University and senior fellow at the Stanford Woods Institute for the Environment. She is a coauthor of the study, which appears in the Journal of Heredity. That research shows that the more gene flow there is among tiger populations, the more genetic diversity is maintained and the higher the chances of species survival become. In fact, it might be possible to maintain tiger populations that preserve about 90 percent of genetic diversity. (via Tigers need diverse gene pool to survive | Futurity)

Tigers need diverse gene pool to survive
Stanford University Original Study


New research shows that increasing genetic diversity among the 3,000 or so tigers left on the planet, though interbreeding and other methods, may be the key to their survival as a species. Iconic symbols of power and beauty, wild tigers may roam only in stories someday soon. Their historical range has been reduced by more than 90 percent. But conservation plans that focus only on increasing numbers and preserving distinct subspecies ignore genetic diversity, according to the study. In fact, following that approach, the tiger could vanish entirely. “Numbers don’t tell the entire story,” says Elizabeth Hadly, professor in environmental biology at Stanford University and senior fellow at the Stanford Woods Institute for the Environment. She is a coauthor of the study, which appears in the Journal of Heredity.
That research shows that the more gene flow there is among tiger populations, the more genetic diversity is maintained and the higher the chances of species survival become. In fact, it might be possible to maintain tiger populations that preserve about 90 percent of genetic diversity. (via Tigers need diverse gene pool to survive | Futurity)