A Momentary Flow

Updating Worldviews one World at a time

Evolution’s Random Paths Lead to One Place - A massive statistical study suggests that the final evolutionary outcome — fitness — is predictable. - In his fourth-floor lab at Harvard University, Michael Desai has created hundreds of identical worlds in order to watch evolution at work. Each of his meticulously controlled environments is home to a separate strain of baker’s yeast. Every 12 hours, Desai’s robot assistants pluck out the fastest-growing yeast in each world — selecting the fittest to live on — and discard the rest. Desai then monitors the strains as they evolve over the course of 500 generations. His experiment, which other scientists say is unprecedented in scale, seeks to gain insight into a question that has long bedeviled biologists: If we could start the world over again, would life evolve the same way? Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s. Desai’s yeast cells call this belief into question. According to results published in Science in June, all of Desai’s yeast varieties arrived at roughly the same evolutionary endpoint (as measured by their ability to grow under specific lab conditions) regardless of which precise genetic path each strain took. It’s as if 100 New York City taxis agreed to take separate highways in a race to the Pacific Ocean, and 50 hours later they all converged at the Santa Monica pier. The findings also suggest a disconnect between evolution at the genetic level and at the level of the whole organism. Genetic mutations occur mostly at random, yet the sum of these aimless changes somehow creates a predictable pattern. The distinction could prove valuable, as much genetics research has focused on the impact of mutations in individual genes. For example, researchers often ask how a single mutation might affect a microbe’s tolerance for toxins, or a human’s risk for a disease. But if Desai’s findings hold true in other organisms, they could suggest that it’s equally important to examine how large numbers of individual genetic changes work in concert over time. “There’s a kind of tension in evolutionary biology between thinking about individual genes and the potential for evolution to change the whole organism,” said Michael Travisano, a biologist at the University of Minnesota. “All of biology has been focused on the importance of individual genes for the last 30 years, but the big take-home message of this study is that’s not necessarily important.” (via Yeast Study Suggests Genetics Are Random but Evolution Is Not | Simons Foundation)

Evolution’s Random Paths Lead to One Place
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A massive statistical study suggests that the final evolutionary outcome — fitness — is predictable.
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In his fourth-floor lab at Harvard University, Michael Desai has created hundreds of identical worlds in order to watch evolution at work. Each of his meticulously controlled environments is home to a separate strain of baker’s yeast. Every 12 hours, Desai’s robot assistants pluck out the fastest-growing yeast in each world — selecting the fittest to live on — and discard the rest. Desai then monitors the strains as they evolve over the course of 500 generations. His experiment, which other scientists say is unprecedented in scale, seeks to gain insight into a question that has long bedeviled biologists: If we could start the world over again, would life evolve the same way? Many biologists argue that it would not, that chance mutations early in the evolutionary journey of a species will profoundly influence its fate. “If you replay the tape of life, you might have one initial mutation that takes you in a totally different direction,” Desai said, paraphrasing an idea first put forth by the biologist Stephen Jay Gould in the 1980s. Desai’s yeast cells call this belief into question. According to results published in Science in June, all of Desai’s yeast varieties arrived at roughly the same evolutionary endpoint (as measured by their ability to grow under specific lab conditions) regardless of which precise genetic path each strain took. It’s as if 100 New York City taxis agreed to take separate highways in a race to the Pacific Ocean, and 50 hours later they all converged at the Santa Monica pier. The findings also suggest a disconnect between evolution at the genetic level and at the level of the whole organism. Genetic mutations occur mostly at random, yet the sum of these aimless changes somehow creates a predictable pattern. The distinction could prove valuable, as much genetics research has focused on the impact of mutations in individual genes. For example, researchers often ask how a single mutation might affect a microbe’s tolerance for toxins, or a human’s risk for a disease. But if Desai’s findings hold true in other organisms, they could suggest that it’s equally important to examine how large numbers of individual genetic changes work in concert over time. “There’s a kind of tension in evolutionary biology between thinking about individual genes and the potential for evolution to change the whole organism,” said Michael Travisano, a biologist at the University of Minnesota. “All of biology has been focused on the importance of individual genes for the last 30 years, but the big take-home message of this study is that’s not necessarily important.” (via Yeast Study Suggests Genetics Are Random but Evolution Is Not | Simons Foundation)

Proteins from pond scum revolutionize neuroscience

See on Scoop.it - The future of medicine and health

I wrote a story recently about a cool technique called optogenetics, developed by bioengineering professor Karl Deisseroth, MD, PhD. He won the Keio Prize in Medicine, and I thought it might be interesting to talk with some other neuroscientists at Stanford to get their take on the importance of the technology. You know something is truly groundbreaking when each and every person you interview uses the word “revolutionary” to describe it.

Optogenetics is a technique that allows scientists to use light to turn particular nerves on or off. In the process, they’re learning new things about how the brain works and about diseases and mental health conditions like Parkinson’s disease, addiction and depression.

In describing the award, the Keio Prize committee wrote:

By making optogenetics a reality and leading this new field, Dr. Deisseroth has made enormous contributions towards the fundamental understanding of brain functions in health and disease.

One of the things I found most interesting when writing the story came from a piece Deisseroth wrote several years ago in Scientific American in which he stressed the importance of basic research. Optogenetics would not have been a reality without discoveries made in the lowly algae that makes up pond scum.

“The more directed and targeted research becomes, the more likely we are to slow our progress, and the more certain it is that the distant and untraveled realms, where truly disruptive ideas can arise, will be utterly cut off from our common scientific journey,” Deisseroth wrote.

Deisseroth told me that we need to be funding basic, curiosity-driven research along with efforts to make those discoveries relevant. He said that kind of translation is part of the value of  programs like Stanford Bio-X – an interdisciplinary institute founded in 1998 – which puts diverse faculty members side by side to enable that translation from basic science to medical discovery.


See on scopeblog.stanford.edu
laboratoryequipment:

Researchers Capture Sound of an AtomResearchers at Chalmers Univ. of Technology have shown the use of sound to communicate with an artificial atom. They can thereby demonstrate phenomena from quantum physics with sound taking on the role of light. The results will be published in the journal Science.The interaction between atoms and light is well known and has been studied extensively in the field of quantum optics. However, to achieve the same kind of interaction with sound waves has been a more challenging undertaking. The Chalmers researchers have now succeeded in making acoustic waves couple to an artificial atom. The study was done in collaboration between experimental and theoretical physicists.Read more: http://www.laboratoryequipment.com/news/2014/09/researchers-capture-sound-atom

laboratoryequipment:

Researchers Capture Sound of an Atom

Researchers at Chalmers Univ. of Technology have shown the use of sound to communicate with an artificial atom. They can thereby demonstrate phenomena from quantum physics with sound taking on the role of light. The results will be published in the journal Science.

The interaction between atoms and light is well known and has been studied extensively in the field of quantum optics. However, to achieve the same kind of interaction with sound waves has been a more challenging undertaking. The Chalmers researchers have now succeeded in making acoustic waves couple to an artificial atom. The study was done in collaboration between experimental and theoretical physicists.

Read more: http://www.laboratoryequipment.com/news/2014/09/researchers-capture-sound-atom

Reblogged from Laboratory Equipment

Could ‘solid’ light compute previously unsolvable problems? - An “artificial atom” makes photons behave like exotic matter  - Researchers at Princeton University have “crystallized” light. They are not shining light through crystal — they are actually transforming light into crystal, as part of an effort to develop exotic materials such as room-temperature superconductors. The researchers locked together photons so that they became fixed in place. “It’s something that we have never seen before,” said Andrew Houck, an associate professor of electrical engineering and one of the researchers. “This is a new behavior for light.” The results raise intriguing possibilities for a variety of future materials, and also address questions in condensed matter physics — the fundamental study of matter. “We are interested in exploring — and ultimately controlling and directing — the flow of energy at the atomic level,” said Hakan Türeci, an assistant professor of electrical engineering and a member of the research team. “The goal is to better understand current materials and processes and to evaluate materials that we cannot yet create.” The team’s findings, reported online Sept. 8 in the journal Physical Review X (open access), are part of an effort to answer fundamental questions about atomic behavior by creating a device that can simulate the behavior of subatomic particles. Special-purpose quantum computers Such a tool could be an invaluable method for answering questions about atoms and molecules that are not answerable even with today’s most advanced computers. In part, that’s because current computers operate under the rules of classical mechanics, while the world of atoms and photons obeys the rules of quantum mechanics, which include a number of strange and very counterintuitive features. One of these odd properties is called “entanglement,” in which multiple particles become linked and can affect each other over long distances. A computer based on the rules of quantum mechanics could help crack problems that are currently unsolvable. But building a general-purpose quantum computer has proven to be incredibly difficult. Another approach, which the Princeton team is taking, is to build a system that directly simulates the desired quantum behavior. Although each machine is limited to a single task, it would allow researchers to answer important questions without having to solve some of the more difficult problems involved in creating a general-purpose quantum computer. The device could also allow physicists to explore fundamental questions about the behavior of matter by mimicking materials that only exist in physicists’ imaginations. (via Could ‘solid’ light compute previously unsolvable problems? | KurzweilAI)

Could ‘solid’ light compute previously unsolvable problems?
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An “artificial atom” makes photons behave like exotic matter
-
Researchers at Princeton University have “crystallized” light. They are not shining light through crystal — they are actually transforming light into crystal, as part of an effort to develop exotic materials such as room-temperature superconductors. The researchers locked together photons so that they became fixed in place. “It’s something that we have never seen before,” said Andrew Houck, an associate professor of electrical engineering and one of the researchers. “This is a new behavior for light.” The results raise intriguing possibilities for a variety of future materials, and also address questions in condensed matter physics — the fundamental study of matter. “We are interested in exploring — and ultimately controlling and directing — the flow of energy at the atomic level,” said Hakan Türeci, an assistant professor of electrical engineering and a member of the research team. “The goal is to better understand current materials and processes and to evaluate materials that we cannot yet create.” The team’s findings, reported online Sept. 8 in the journal Physical Review X (open access), are part of an effort to answer fundamental questions about atomic behavior by creating a device that can simulate the behavior of subatomic particles. Special-purpose quantum computers Such a tool could be an invaluable method for answering questions about atoms and molecules that are not answerable even with today’s most advanced computers. In part, that’s because current computers operate under the rules of classical mechanics, while the world of atoms and photons obeys the rules of quantum mechanics, which include a number of strange and very counterintuitive features. One of these odd properties is called “entanglement,” in which multiple particles become linked and can affect each other over long distances. A computer based on the rules of quantum mechanics could help crack problems that are currently unsolvable. But building a general-purpose quantum computer has proven to be incredibly difficult. Another approach, which the Princeton team is taking, is to build a system that directly simulates the desired quantum behavior. Although each machine is limited to a single task, it would allow researchers to answer important questions without having to solve some of the more difficult problems involved in creating a general-purpose quantum computer. The device could also allow physicists to explore fundamental questions about the behavior of matter by mimicking materials that only exist in physicists’ imaginations. (via Could ‘solid’ light compute previously unsolvable problems? | KurzweilAI)

Fungus Could Be the Key to Avoiding a Global Food Crisis - Our world is sitting on time bomb.
According to a United Nations report, climate change is poised to decimate the global food supply, with agricultural production expected to decline as much as 2 percent each decade for the rest of this century. Meanwhile, the world population will only increase, almost certainly driving up demand for these crops by as much as 14 percent every decade. That means food prices will soar, communities plagued by hunger will go even hungrier, and, many experts fear, countries will fight for food, just as they have for oil. The good news is unorthodox companies like Adaptive Symbiotic Technologies are working to reverse this harrowing trend. The Seattle startup, founded in 2008, has developed an organic seed treatment it calls BioEnsure that allows agricultural crops like rice and corn to withstand severe droughts and extreme temperatures. It’s based on fungi that company CEO Dr. Rusty Rodriguez and his wife, Dr. Regina Redman, discovered some 20 years ago, that enables plants to grow in extreme heat. After spending decades perfecting and field-testing the formulation, Adaptive is preparing to bring BioEnsure to market this fall. It’s an innovation that, if successfully adopted by the agricultural industry, could not only help ensure global food safety, but reduce our dependence on harmful chemicals. “We believe it holds the potential to improve the lives of millions of people who need to produce food in difficult conditions,” says Christian Holmes, global water coordinator at United States Agency for International Development, or USAID, the government agency that helps provide aid to foreign countries. Adaptive recently was chosen as one of 17 nominees for USAID’s Securing Water for Food Grand Challenge, a partnership between USAID and the governments of Sweden and the Netherlands, which will award $32 million in funding to innovations in the water and food security space. “We reject the idea that there’s a point of no return,” Holmes says. “What we need are breakthrough solutions like this that can reach millions of people really quickly.” (via Fungus Could Be the Key to Avoiding a Global Food Crisis | WIRED)

Fungus Could Be the Key to Avoiding a Global Food Crisis
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Our world is sitting on time bomb.

According to a United Nations report, climate change is poised to decimate the global food supply, with agricultural production expected to decline as much as 2 percent each decade for the rest of this century. Meanwhile, the world population will only increase, almost certainly driving up demand for these crops by as much as 14 percent every decade. That means food prices will soar, communities plagued by hunger will go even hungrier, and, many experts fear, countries will fight for food, just as they have for oil. The good news is unorthodox companies like Adaptive Symbiotic Technologies are working to reverse this harrowing trend. The Seattle startup, founded in 2008, has developed an organic seed treatment it calls BioEnsure that allows agricultural crops like rice and corn to withstand severe droughts and extreme temperatures. It’s based on fungi that company CEO Dr. Rusty Rodriguez and his wife, Dr. Regina Redman, discovered some 20 years ago, that enables plants to grow in extreme heat. After spending decades perfecting and field-testing the formulation, Adaptive is preparing to bring BioEnsure to market this fall. It’s an innovation that, if successfully adopted by the agricultural industry, could not only help ensure global food safety, but reduce our dependence on harmful chemicals. “We believe it holds the potential to improve the lives of millions of people who need to produce food in difficult conditions,” says Christian Holmes, global water coordinator at United States Agency for International Development, or USAID, the government agency that helps provide aid to foreign countries.
Adaptive recently was chosen as one of 17 nominees for USAID’s Securing Water for Food Grand Challenge, a partnership between USAID and the governments of Sweden and the Netherlands, which will award $32 million in funding to innovations in the water and food security space. “We reject the idea that there’s a point of no return,” Holmes says. “What we need are breakthrough solutions like this that can reach millions of people really quickly.” (via Fungus Could Be the Key to Avoiding a Global Food Crisis | WIRED)

Activating gene in key organ systems slows aging process throughout the body

See on Scoop.it - The future of medicine and health

With a typical lifespan of around six weeks, the common fruit fly is one animal that could benefit from a slowing of the aging process. And that’s just what a team of biologists at UCLA have achieved by activating a gene called AMPK. Possibly of more interest to us higher life forms is the researchers’ belief that the discovery could help delay aging and age-related diseases in humans.

AMPK (adenosine monophosphate-activated protein kinase) is an enzyme that acts as a metabolic master switch and is activated in response to low cellular energy levels. It has previously been shown to activate a cellular process known as autophagy, which protects against aging by enabling cells to degrade and discard old, damaged “cellular garbage” before it damages cells. Although AMPK is also found in humans, it is not usually activated at a high level.

The UCLA research team found that increasing the amount of AMPK in the intestines of common fruit flies (Drosophila melanogaster) increased their lifespan by around 30 percent, up from the typical six weeks to around eight weeks. Importantly, the fruit flies stayed healthier for longer as well, with the beneficial effects not restricted to the organ where it was activated.

"We have shown that when we activate the gene in the intestine or the nervous system, we see the aging process is slowed beyond the organ system in which the gene is activated," said David Walker, an associate professor of integrative biology and physiology at UCLA and senior author of the research.

"A really interesting finding was when Matt (lead author of the study, Matthew Ulgherait) activated AMPK in the nervous system, he saw evidence of increased levels of autophagy in not only the brain, but also in the intestine,” adds Walker. "And vice versa: Activating AMPK in the intestine produced increased levels of autophagy in the brain – and perhaps elsewhere, too."


See on gizmag.com

Guidelines for respectful, constructive, and inclusive philosophical discussion

Compiled by David Chalmers

The guidelines below are intended primarily for oral philosophical discussion in formal settings: colloquia, conferences, seminars, classes, and so on. Many of them have some application to informal philosophical discussion as well.

The specific norms are intended as means of facilitating more general norms of being respectful, constructive, and inclusive. These probably aren’t categorical norms and there are situations in which it is appropriate to violate them, but nevertheless in many philosophical contexts they are useful norms to have in place. Groups are encouraged to adapt and modify these guidelines for their purposes as they see fit.

All this is a highly tentative work in progress. Suggestions for addition, subtraction, and change are more than welcome. Thanks to many philosophers for their suggestions so far.

I. Norms of respect

1. Be nice

2. Don’t interrupt.

3. Don’t present objections as flat dismissals (leave open the possibility that there’s a response).

4. Don’t be incredulous.

5. Don’t roll your eyes, make faces, laugh at a participant, etc, especially to others on the side. (Partial exception for signalling norm violations to the chair.)

6. Don’t start side conversations parallel to the main discussion.

7. Acknowledge your interlocutor’s insights.

8. Object to theses, don’t object to people.

II. Norms of constructiveness

1. Objections are fine, but it’s also always OK to be constructive, building on a speaker’s project or strengthening their position. Even objections can often be cast in a constructive way.

2. Even when an objection is destructive with respect to a position, it often helps to find a positive insight suggested by the objection.

3. If you find yourself thinking that the project is worthless and there is nothing to be learned from it, think twice before asking your question.

4. It’s OK to question the presuppositions of a project or an area, but discussions in which these questions dominate can be unhelpful.

5. You don’t need to keep pressing the same objection (individually or collectively) until the speaker says uncle.

6. Remember that philosophy isn’t a zero-sum game. (Related version: philosophy isn’t Fight Club.)  

III. Norms of inclusiveness:

1. Don’t dominate the discussion (partial exception for the speaker here!).

2. Raise one question per question (further questions go to the back of the queue).

3. Don’t let your question (or your answer) run on forever.

4. Acknowledge points made by previous questioners.

5. It’s OK to ask a question that you think may be obtuse or uninformed.

6. Don’t use unnecessarily offensive examples.

IV. Procedural norms (for Q&A after talks; some are specific to the hand/finger system)

1. If there’s time, take a 3-5 minute break before Q&A (for resting, leaving, and formulating questions). Hold back questions until after the break.

2. The chair rather than the speaker should field questions (to avoid various biases), and the chair should keep a list of questioners.

3. To raise a new question at any point, raise your hand until the chair acknowledges you and adds you to the list. To follow up on an existing question by someone else, raise your finger.

4. Unless you’re speaker, existing questioner, or chair, don’t speak without being called on (limited exceptions for occasional jokes and other very brief interjections, not to be abused).

5. Following up your own question is usually fine (unless time is short), but follow-up rounds should usually be increasingly brief, and think twice about whether third and later rounds are really needed.

6. Follow-ups should pick up directly on the existing discussion, rather than being tangentially or distantly related (for follow-ups of that sort, raise your hand).

7. The chair should attempt to balance the discussion among participants, prioritizing those who have not spoken before (it isn’t mandatory to call on people in the order of seeing them).

8. The chair should try to pace things so that everyone who has a question can ask a question. In short discussion periods, or with a short time remaining, this may be difficult; disallowing fingers helps.  

V. Metanorms

1. When norms are violated, the chair is encouraged to gently point this out, and others should feel free to say something or to signal the chair.

2. If it’s more comfortable to do so, it’s also fine to quietly point out violations after the seminar (or to tell the chair who can talk to the offender).

3. If the chair violates the norms, feel free to say so then or afterwards.

4. Try not to be defensive when a violation is pointed out.

5. Remember that it’s quite possible to violate these norms without being a bad person. (I’ve certainly violated most of them myself.)

6. Respect the chair’s enforcement of these norms.

7. Policing usually works better with a light touch.

VI. Potential additional norms (mostly suggested by others; for various reasons I haven’t included them on the canonical list, but I’m sympathetic with many of them, and they’re certainly worth considering)

1. Maximum two minutes per question (modified version: after two minutes, interruptions are OK).

2. Prioritize junior people in calling on questions (modified version: don’t prioritize senior people).

3. Ask permission to follow up your own question (modified version: ask permission for any follow-up after the first).

4. Don’t worry about impressing people.

5. Be cautious about pestering the speaker during the break or after the talk (they may need to rest).

6. Negotiate these norms as a group at the start of a course or related activity.

Related resources (and sources)

Ozone layer showing ‘signs of recovery’, UN says
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The ozone layer that shields the earth from cancer-causing ultraviolet rays is showing early signs of thickening after years of depletion, a UN study says. The ozone hole that appears annually over Antarctica has also stopped growing bigger every year. The report says it will take a decade before the hole starts to shrink. Scientists say the recovery is entirely due to political determination to phase out the man-made CFC gases destroying ozone. The study was published by researchers from the World Meteorological Organization (WMO) and the UN Environment Programme (UNEP). “International action on the ozone layer is a major environmental success story… This should encourage us to display the same level of urgency and unity to tackle the even greater challenge of tackling climate change,” said WMO Secretary-General Michel Jarraud. Dr Ken Jucks from the US space agency Nasa told BBC News that humans “have started to do the right thing in order to convert the atmosphere back towards what it was before the industrial revolution started”. Scientists cannot be absolutely certain yet that the hole will heal itself. Prof David Vaughan from the British Antarctic Survey (BAS) said that test results from his organisation would throw extra light on the WMO’s findings. (via BBC News - Ozone layer showing ‘signs of recovery’, UN says)

In his 2014 book, Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life, top synthetic biologist J. Craig Venter offers powerful words supporting a future shaped by ubiquitous synthetic biology in our lives:
“I can imagine designing simple animal forms that provide novel sources of nutrients and pharmaceuticals, customizing human stem cells to regenerate a damaged, old, or sick body. There will also be new ways to enhance the human body as well, such as boosting intelligence, adapting it to new environments such as radiation levels encountered in space, rejuvenating worn-out muscles, and so on”

An open source future for synthetic biology