Biology and Medicine

Advances in the investigation of the physical universe we live in.
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Enki
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Re: Biology and Medicine

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Men often oppose a thing merely because they have had no agency in planning it, or because it may have been planned by those whom they dislike.
-Alexander Hamilton
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Parodite
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Re: Biology and Medicine

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Deep down I'm very superficial
noddy
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Re: Biology and Medicine

Post by noddy »

from the plots of old horror stories department.

http://www.newscientist.com/article/mg2 ... youth.html
HUMANS are constantly searching for an elixir of youth - could it be that an infusion of young blood holds the key?

This seems to be true for mice, at least. According to research presented this week at the Society for Neuroscience conference in New Orleans, Louisiana, giving young blood to old mice can reverse some of the effects of age-related cognitive decline.

Last year, Saul Villeda, then at Stanford University in California, and colleagues showed they could boost the growth of new cells in the brains of old mice by giving them a blood infusion from young mice (Nature, doi.org/c9jwvm).

"We know that blood has this huge effect on brain cells, but we didn't know if its effects extended beyond cell regeneration," he says.

Now the team has tested for changes in cognition by linking the circulatory systems of young and old mice. Once the blood of each conjoined mouse had fully mixed with the other, the researchers analysed their brains.

Tissue from the hippocampus of old mice given young blood showed changes in the expression of 200 to 300 genes, particularly in those involved in synaptic plasticity, which underpins learning and memory. They also found changes in some proteins involved in nerve growth.

The infusion of young blood also boosted the number and strength of neuronal connections in an area of the brain where new cells do not grow. This didn't happen when old mice received old blood.
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Re: Biology and Medicine

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May the gods preserve and defend me from self-righteous altruists; I can defend myself from my enemies and my friends.
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Antipatros
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Re: Biology and Medicine

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bSidnKdH5_4

Ken Kamler, Medical Miracle on Everest (2009)

http://archive.org/details/KenKamler_2009P
When the worst disaster in the history of Mount Everest climbs occurred, Ken Kamler was the only doctor on the mountain. At TEDMED, he shares the incredible story of the climbers' battle against extreme conditions and uses brain imaging technology to map the medical miracle of one man who survived roughly 36 hours buried in the snow.
Be not too curious of Good and Evil;
Seek not to count the future waves of Time;
But be ye satisfied that you have light
Enough to take your step and find your foothold.

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Endovelico
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Re: Biology and Medicine

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Breakthrough Nanoparticle Halts Multiple Sclerosis in Mice, Offers Hope for Other Immune-Related Diseases

ScienceDaily (Nov. 18, 2012) — In a breakthrough for nanotechnology and multiple sclerosis, a biodegradable nanoparticle turns out to be the perfect vehicle to stealthily deliver an antigen that tricks the immune system into stopping its attack on myelin and halt a model of relapsing remitting multiple sclerosis (MS) in mice, according to new Northwestern Medicine research.

The new nanotechnology also can be applied to a variety of immune-mediated diseases including Type 1 diabetes, food allergies and airway allergies such as asthma.

In MS, the immune system attacks the myelin membrane that insulates nerves cells in the brain, spinal cord and optic nerve. When the insulation is destroyed, electrical signals can't be effectively conducted, resulting in symptoms that range from mild limb numbness to paralysis or blindness. About 80 percent of MS patients are diagnosed with the relapsing remitting form of the disease.

The Northwestern nanotechnology does not suppress the entire immune system as do current therapies for MS, which make patients more susceptible to everyday infections and higher rates of cancer. Rather, when the nanoparticles are attached to myelin antigens and injected into the mice, the immune system is reset to normal. The immune system stops recognizing myelin as an alien invader and halts its attack on it.

"This is a highly significant breakthrough in translational immunotherapy," said Stephen Miller, a corresponding author of the study and the Judy Gugenheim Research Professor of Microbiology-Immunology at Northwestern University Feinberg School of Medicine. "The beauty of this new technology is it can be used in many immune-related diseases. We simply change the antigen that's delivered."

"The holy grail is to develop a therapy that is specific to the pathological immune response, in this case the body attacking myelin," Miller added. "Our approach resets the immune system so it no longer attacks myelin but leaves the function of the normal immune system intact."

The nanoparticle, made from an easily produced and already FDA-approved substance, was developed by Lonnie Shea, professor of chemical and biological engineering at Northwestern's McCormick School of Engineering and Applied Science.

"This is a major breakthrough in nanotechnology, showing you can use it to regulate the immune system," said Shea, also a corresponding author. The paper will be published Nov. 18 in the journal Nature Biotechnology.

Miller and Shea are also members of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University. In addition, Shea is a member of the Institute for BioNanotechnology in Medicine and the Chemistry of Life Processes Institute.

Clinical Trial for Ms Tests Same Approach -- With Key Difference

The study's method is the same approach now being tested in multiple sclerosis patients in a phase I/II clinical trial -- with one key difference. The trial uses a patient's own white blood cells -- a costly and labor intensive procedure -- to deliver the antigen. The purpose of the new study was to see if nanoparticles could be as effective as the white blood cells as delivery vehicles. They were.

The Big Nanoparticle Advantage for Immunotherapy

Nanoparticles have many advantages; they can be readily produced in a laboratory and standardized for manufacturing. They would make the potential therapy cheaper and more accessible to a general population. In addition, these nanoparticles are made of a polymer called Poly(lactide-co-glycolide) (PLG), which consists of lactic acid and glycolic acid, both natural metabolites in the human body. PLG is most commonly used for biodegradable sutures.

The fact that PLG is already FDA approved for other applications should facilitate translating the research to patients, Shea noted. Miller and Shea tested nanoparticles of various sizes and discovered that 500 nanometers was most effective at modulating the immune response.

"We administered these particles to animals who have a disease very similar to relapsing remitting multiple sclerosis and stopped it in its tracks," Miller said. "We prevented any future relapses for up to 100 days, which is the equivalent of several years in the life of an MS patient."

Shea and Miller also are currently testing the nanoparticles to treat Type one diabetes and airway diseases such as asthma.

Nanoparticles Fool Immune System

In the study, researchers attached myelin antigens to the nanoparticles and injected them intravenously into the mice. The particles entered the spleen, which filters the blood and helps the body dispose of aging and dying blood cells. There, the particles were engulfed by macrophages, a type of immune cell, which then displayed the antigens on their cell surface. The immune system viewed the nanoparticles as ordinary dying blood cells and nothing to be concerned about. This created immune tolerance to the antigen by directly inhibiting the activity of myelin responsive T cells and by increasing the numbers of regulatory T cells which further calmed the autoimmune response.

"The key here is that this antigen/particle-based approach to induction of tolerance is selective and targeted. Unlike generalized immunosuppression, which is the current therapy used for autoimmune diseases, this new process does not shut down the whole immune system," said Christine Kelley, National Institute of Biomedical Imaging and Bioengineering director of the division of Discovery Science and Technology at the National Institutes of Health, which supported the research. "This collaborative effort between expertise in immunology and bioengineering is a terrific example of the tremendous advances that can be made with scientifically convergent approaches to biomedical problems."

"We are proud to share our expertise in therapeutics development with Dr. Stephen Miller's stellar team of academic scientists," said Scott Johnson, CEO, president and founder of the Myelin Repair Foundation. "The idea to couple antigens to nanoparticles was conceived in discussions between Dr. Miller's laboratory, the Myelin Repair Foundation's drug discovery advisory board and Dr. Michael Pleiss, a member of the Myelin Repair Foundation's internal research team, and we combined our efforts to focus on patient-oriented, clinically relevant research with broad implications for all autoimmune diseases. Our unique research model is designed to foster and extract the innovation from the academic science that we fund and transition these technologies to commercialization. The overarching goal is to ensure this important therapeutic pathway has its best chance to reach patients, with MS and all autoimmune diseases."

http://www.sciencedaily.com/releases/20 ... 141516.htm
Soon we will have trouble dying...
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Typhoon
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Re: Biology and Medicine

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May the gods preserve and defend me from self-righteous altruists; I can defend myself from my enemies and my friends.
Crocus sativus

Re: Biology and Medicine

Post by Crocus sativus »

.

Sperm count of French men drops sharply by 32%, may signal larger decline


Researchers found that between 1989 and 2005, the number of sperm in one millilitre of the average 35-year-old Frenchman’s semen fell from about 74 million to about 50 million — a decrease of roughly 32%.

[..]

The researchers also found that there was an increase in the number of abnormally shaped sperm over the study period, which can also influence fertility.

.
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Nonc Hilaire
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Re: Biology and Medicine

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Crocus sativus wrote:.

Sperm count of French men drops sharply by 32%, may signal larger decline


Researchers found that between 1989 and 2005, the number of sperm in one millilitre of the average 35-year-old Frenchman’s semen fell from about 74 million to about 50 million — a decrease of roughly 32%.

[..]

The researchers also found that there was an increase in the number of abnormally shaped sperm over the study period, which can also influence fertility.
Roughly corresponds with the opening of Disneyland Paris.


.
“Christ has no body now but yours. Yours are the eyes through which he looks with compassion on this world. Yours are the feet with which he walks among His people to do good. Yours are the hands through which he blesses His creation.”

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Azrael
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Re: Biology and Medicine

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DNA Study Shows Romani (Gypsies) are from India

Image
Ceferino Giménez Malla -- Patron Saint of Romani
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Apollonius
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Re: Biology and Medicine

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In a girl's last hope, altered immune cells beat leukemia - Denise Grady, New York Times, 10 December 2012
http://www.nytimes.com/2012/12/10/healt ... cells.html


PHILIPSBURG, Pa. — Emma Whitehead has been bounding around the house lately, practicing somersaults and rugby-style tumbles that make her parents wince.

It is hard to believe, but last spring Emma, then 6, was near death from leukemia. She had relapsed twice after chemotherapy, and doctors had run out of options.

Desperate to save her, her parents sought an experimental treatment at the Children’s Hospital of Philadelphia, one that had never before been tried in a child, or in anyone with the type of leukemia Emma had. The experiment, in April, used a disabled form of the virus that causes AIDS to reprogram Emma’s immune system genetically to kill cancer cells.

The treatment very nearly killed her. But she emerged from it cancer-free, and about seven months later is still in complete remission. She is the first child and one of the first humans ever in whom new techniques have achieved a long-sought goal — giving a patient’s own immune system the lasting ability to fight cancer.
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Early Man Made Cheese

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PARIS — Pre-historic man was already making cheese some 7,000 years ago, using perforated clay pots as strainers, scientists said Wednesday.
Cheese production would have been a key development in human history, allowing the preservation of milk in a non-perishable, transportable and more digestible form, said a report in the journal Nature.
Scientists have long speculated that pierced potsherds discovered at Neolithic-era sites around northern Europe may be from cheese strainers.
An international team said Wednesday they found proof for this theory from chemical analysis of fatty acid deposits on unglazed pottery pieces excavated in Poland, dating from about 7,000 years ago.
"The presence of abundant milk fat in these specialised vessels, comparable in form to modern cheese strainers, provides compelling evidence for the vessels having been used to separate fat-rich milk curds from the lactose-containing whey," the researchers wrote.
Early farmers would have been lactose intolerant, lacking the genetic mutation we have since acquired to digest milk products long after being weaned off the breast.

Who knew prehistoric polish people were so smart?
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Endovelico
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Re: Biology and Medicine

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Stem Cells Found to Heal Damaged Artery in Lab Study in Baboons

Jan. 10, 2013 — Scientists at the Texas Biomedical Research Institute in San Antonio have for the first time demonstrated that baboon embryonic stem cells can be programmed to completely restore a severely damaged artery. These early results show promise for eventually developing stem cell therapies to restore human tissues or organs damaged by age or disease.

"We first cultured the stem cells in petri dishes under special conditions to make them differentiate into cells that are the precursors of blood vessels, and we saw that we could get them to form tubular and branching structures, similar to blood vessels," said John L. VandeBerg, Ph.D., Texas Biomed's chief scientific officer.

This finding gave VandeBerg and his team the confidence to do complex experiments to find out if these cells could actually heal a damaged artery. Human embryonic stem cells were first isolated and grown in 1998.

The results are presented in a manuscript, co-authored by Texas Biomed's Qiang Shi, Ph.D., and Gerald Shatten, Ph.D., of the University of Pittsburgh, published in the January 10, 2013 issue of the Journal of Cellular and Molecular Medicine.

The scientists found that cells derived from embryonic stem cells could actually repair experimentally damaged baboon arteries and "are promising therapeutic agents for repairing damaged vasculature of people," according to the authors.

Researchers completely removed the cells that line the inside surface from a segment of artery, and then put cells that had been derived from embryonic stem cells inside the artery. They then connected both ends of the arterial segment to plastic tubing inside a device called a bioreactor which is designed to grow cells and tissues. The scientists then pumped fluid through the artery under pressure as if blood were flowing through it.

The outside of the artery was bathed in another fluid to sustain the cells located there. Three days later, the complex structure of the inner surface was beginning to regenerate, and by 14 days, the inside of the artery had been perfectly restored to its complex natural state. It went from a non-functional tube to a complex fully functional artery.

"Just think of what this kind of treatment would mean to a patient who had just suffered a heart attack as a consequence of a damaged coronary artery. And this is the real potential of stem cell regenerative medicine -- that is, a treatment with stem cells that regenerates a damaged or destroyed tissue or organ," VandeBerg said.

To show that the artery couldn't heal itself in the absence of stem cells, the researchers took a control arterial segment that also was stripped of the cells on its interior surface, but did not seed it with stem cells. No healing occurred.

Stains for proteins that indicate functional characteristics showed that the healed artery had completely normal function and could do everything that a normal artery does in a healthy individual.

"This is evidence that we can harness stem cells to treat the gravest of arterial injuries," said VandeBerg.

Eventually, scientists hope to be able to take a skin cell or a white blood cell or a cell from any other tissue in the body, and induce it to become just like an embryonic stem cell in its capacity to differentiate into any tissue or organ.

"The vision of the future is, for example, for a patient with a pancreas damaged because of diabetes, doctors could take skin cells, induce them to become stem cells, and then grow a new pancreas that is just like the one before disease developed," VandeBerg said.

http://www.sciencedaily.com/releases/20 ... 161150.htm
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Elizabeth takes a Blood Bath, Dracula Catches AIDS.......

Post by monster_gardener »

noddy wrote:from the plots of old horror stories department.

http://www.newscientist.com/article/mg2 ... youth.html
HUMANS are constantly searching for an elixir of youth - could it be that an infusion of young blood holds the key?

This seems to be true for mice, at least. According to research presented this week at the Society for Neuroscience conference in New Orleans, Louisiana, giving young blood to old mice can reverse some of the effects of age-related cognitive decline.

Last year, Saul Villeda, then at Stanford University in California, and colleagues showed they could boost the growth of new cells in the brains of old mice by giving them a blood infusion from young mice (Nature, doi.org/c9jwvm).

"We know that blood has this huge effect on brain cells, but we didn't know if its effects extended beyond cell regeneration," he says.

Now the team has tested for changes in cognition by linking the circulatory systems of young and old mice. Once the blood of each conjoined mouse had fully mixed with the other, the researchers analysed their brains.

Tissue from the hippocampus of old mice given young blood showed changes in the expression of 200 to 300 genes, particularly in those involved in synaptic plasticity, which underpins learning and memory. They also found changes in some proteins involved in nerve growth.

The infusion of young blood also boosted the number and strength of neuronal connections in an area of the brain where new cells do not grow. This didn't happen when old mice received old blood.
Thank You VERY MUCH for your post, Noddy.

So it seems Bloody Countess Elizabeth Bathory was right........... ;) :shock: :twisted: :roll:

http://en.wikipedia.org/wiki/Elizabeth_B%C3%A1thory

And Drac would have been right too..........

If he hadn't caught AIDS & Hepatitis B plus gotten stoned out of his his gourd when he started preying on the party crowd......... 8-) :lol:
For the love of G_d, consider you & I may be mistaken.
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Re: Biology and Medicine

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http://www.bloomberg.com/news/2013-01-1 ... ealth.html
Pubic lice, the crab-shaped insects that have dwelled in human groins since the beginning of history, are disappearing. Doctors say bikini waxing may be the reason.
Waning infestations of the bloodsuckers have been linked by doctors to pubic depilation, especially a technique popularized in the 1990s by a Manhattan salon run by seven Brazilian sisters. More than 80 percent of college students in the U.S. remove all or some of their pubic hair -- part of a trend that’s increasing in western countries. In Australia, Sydney’s main sexual health clinic hasn’t seen a woman with pubic lice since 2008 and male cases have fallen 80 percent from about 100 a decade ago.
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In praise of Chinese eugenics

Post by Huxley »

Edge.org: 2013 : WHAT *SHOULD* WE BE WORRIED ABOUT?

Geoffrey Miller | Chinese Eugenics

Geoffrey Miller, an evolutionary psychologist at NYU Stern Business School, warns that China's embrace of eugenic policies will produce a nation of genetically enhanced Übermenschen that will leave the West in the dust. He catalogs the horrors - the one-child policy, which he believes is partly aimed at reducing "dysgenic fertility among rural peasants" and which, he notes, can be circumvented by the wealthy; a 1995 law prohibiting the genetically defective from marrying; the prospect of using preimplantation embryo selection to boost the national IQ and create a "utopian Han ethno-state"; he neglects to mention forced abortion and sterilization. It's a country and a government that will, apparently, brutally suppress individual rights in the pursuit of national aggrandizement through population control and cutting-edge biotechnology. The only sensible Western response to all this is, of course.......... uncritical emulation!

Wait, what?
Geoffrey Miller wrote:My real worry is the Western response. The most likely response, given Euro-American ideological biases, would be a bioethical panic that leads to criticism of Chinese population policy with the same self-righteous hypocrisy that we have shown in criticizing various Chinese socio-cultural policies. But the global stakes are too high for us to act that stupidly and short-sightedly. A more mature response would be based on mutual civilizational respect, asking—what can we learn from what the Chinese are doing, how can we help them, and how can they help us to keep up as they create their brave new world?
Miller seems blithely unaware of the disturbing implications of what he is advocating. His article displays not a hint of concern about, or even awareness of, the possible ethical and social problems arising from the unfettered use of eugenics by a lawless dictatorship. Miller does not seem cognizant either of the various interesting historical expressions of eugenics in the West. I have to wonder whether he is having a bit of a laugh at our expense. Surely no one can use the phrase "brave new world" approvingly and without irony...?

To those of you who are more clued in, is this guy (assuming he is serious) just an aberration, or is this type of thinking becoming common in the U.S. and Europe?
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Azrael
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Re: Biology and Medicine

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noddy wrote:http://www.bloomberg.com/news/2013-01-1 ... ealth.html
Pubic lice, the crab-shaped insects that have dwelled in human groins since the beginning of history, are disappearing. Doctors say bikini waxing may be the reason.
Waning infestations of the bloodsuckers have been linked by doctors to pubic depilation, especially a technique popularized in the 1990s by a Manhattan salon run by seven Brazilian sisters. More than 80 percent of college students in the U.S. remove all or some of their pubic hair -- part of a trend that’s increasing in western countries. In Australia, Sydney’s main sexual health clinic hasn’t seen a woman with pubic lice since 2008 and male cases have fallen 80 percent from about 100 a decade ago.
Perhaps bikini waxing should be covered by health insurance. :wink:
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Re: In praise of Chinese eugenics

Post by Typhoon »

Huxley wrote:Edge.org: 2013 : WHAT *SHOULD* WE BE WORRIED ABOUT?

Geoffrey Miller | Chinese Eugenics

Geoffrey Miller, an evolutionary psychologist at NYU Stern Business School, warns that China's embrace of eugenic policies will produce a nation of genetically enhanced Übermenschen that will leave the West in the dust. He catalogs the horrors - the one-child policy, which he believes is partly aimed at reducing "dysgenic fertility among rural peasants" and which, he notes, can be circumvented by the wealthy; a 1995 law prohibiting the genetically defective from marrying; the prospect of using preimplantation embryo selection to boost the national IQ and create a "utopian Han ethno-state"; he neglects to mention forced abortion and sterilization. It's a country and a government that will, apparently, brutally suppress individual rights in the pursuit of national aggrandizement through population control and cutting-edge biotechnology. The only sensible Western response to all this is, of course.......... uncritical emulation!

Wait, what?
Geoffrey Miller wrote:My real worry is the Western response. The most likely response, given Euro-American ideological biases, would be a bioethical panic that leads to criticism of Chinese population policy with the same self-righteous hypocrisy that we have shown in criticizing various Chinese socio-cultural policies. But the global stakes are too high for us to act that stupidly and short-sightedly. A more mature response would be based on mutual civilizational respect, asking—what can we learn from what the Chinese are doing, how can we help them, and how can they help us to keep up as they create their brave new world?
Miller seems blithely unaware of the disturbing implications of what he is advocating. His article displays not a hint of concern about, or even awareness of, the possible ethical and social problems arising from the unfettered use of eugenics by a lawless dictatorship. Miller does not seem cognizant either of the various interesting historical expressions of eugenics in the West. I have to wonder whether he is having a bit of a laugh at our expense. Surely no one can use the phrase "brave new world" approvingly and without irony...?

To those of you who are more clued in, is this guy (assuming he is serious) just an aberration, or is this type of thinking becoming common in the U.S. and Europe?
Don't know if this widespread in academia in the West, but it seems like an odd goal.

I don't of any high level human process that has been pinpointed to a set of genes.

The most recent advance is in instinctive burrowing behaviour in mice.

Gordon Research Conference | Genes & Behavior
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Re: Biology and Medicine

Post by Typhoon »

Azrael wrote:
noddy wrote:http://www.bloomberg.com/news/2013-01-1 ... ealth.html
Pubic lice, the crab-shaped insects that have dwelled in human groins since the beginning of history, are disappearing. Doctors say bikini waxing may be the reason.
Waning infestations of the bloodsuckers have been linked by doctors to pubic depilation, especially a technique popularized in the 1990s by a Manhattan salon run by seven Brazilian sisters. More than 80 percent of college students in the U.S. remove all or some of their pubic hair -- part of a trend that’s increasing in western countries. In Australia, Sydney’s main sexual health clinic hasn’t seen a woman with pubic lice since 2008 and male cases have fallen 80 percent from about 100 a decade ago.
Perhaps bikini waxing should be covered by health insurance. :wink:
Fashion kills . . . lice.
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Re: Biology and Medicine

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May the gods preserve and defend me from self-righteous altruists; I can defend myself from my enemies and my friends.
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Re: Biology and Medicine

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Genes from nowhere: Orphans with a surprising story
24 January 2013 by Helen Pilcher

Many of our genes have no obvious relatives or evolutionary history. So where did they come from?

NOT having any family is tough. Often unappreciated and uncomfortably different, orphans have to fight to fit in and battle against the odds to realise their potential. Those who succeed, from Aristotle to Steve Jobs, sometimes change the world.

Who would have thought that our DNA plays host to a similar cast of foundlings? When biologists began sequencing genomes, they discovered that up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers, and a few even seem have played a part in the evolution of the human brain.

But where do they come from? With no obvious ancestry, it was as if these genes had appeared from nowhere, but that couldn't be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven't - quite the opposite, in fact.

Ever since we discovered genes, biologists have been pondering their origins. At the dawn of life, the very first genes must have been thrown up by chance. But life almost certainly began in an RNA world, so back then, genes weren't just blueprints for making enzymes that guide chemical reactions - they themselves were the enzymes. If random processes threw up a piece of RNA that could help make more copies of itself, natural selection would have kicked in straight away.

As living cells evolved, though, things became much more complex. A gene became a piece of DNA coding for a protein. For a protein to be made, an RNA copy of the DNA has to be created. This cannot happen without "DNA switches", which are actually just extra bits of DNA alongside the protein-coding bits saying "copy this DNA into RNA". Next, the RNA has to get to the protein-making factories. In complex cells, this requires the presence of yet more extra sequences, which act as labels saying "export me" and "start making the protein from here".

The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesimally small. As the French biologist François Jacob famously wrote 35 years ago, "the probability that a functional protein would appear de novo by random association of amino acids is practically zero".

Instead, back in the 1970s it was suggested that the accidental copying of genes can result in a single gene giving rise to a whole family of genes, rather like the way animals branch into families of related species over time. It's common for entire genes to be inadvertently duplicated. Spare copies are usually lost, but sometimes the duplicates come to share the function of the original gene between them, or one can diverge and take on a new function.

Take the light-sensing pigments known as opsins. The various opsins in our eyes are not just related to each other, they are also related to the opsins found in all other animals, from jellyfish to insects. The thousands of different opsin genes found across the animal kingdom all evolved by duplication, starting with a single gene in a common ancestor living around 700 million years ago.

Most genes belong to similar families, and their ancestry can be traced back many millions of years. But when the yeast genome was sequenced around 15 years ago, it was discovered that around a third of yeast genes appeared to have no family. The term orphans (sometimes spelt ORFans) was used to describe individual genes, or small groups of very similar genes, with no known relatives.

"If you see a gene and you can't find a relative you get suspicious," says Ken Weiss, who studies the evolution of complex traits at Penn State University. Some suggested orphans were the genetic equivalent of living fossils like the coelacanth, the last surviving members of an ancient family. Others thought they were nothing special, just normal genes whose family hadn't been found yet. After all, the sequencing of entire genomes had only just begun.

So many orphans

But as the genomes of more and more organisms were sequenced, genetic family reunions proved to be the exception rather than the rule. Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.

The study of orphan genes is still in its infancy, and we know very little about most of them. Those we do know about are a mixed bag. Some are involved with the repair and organisation of DNA, or in controlling the activity of other genes. The insect orphan flightin, which encodes a muscular wing protein, evolved to aid flight. And in a study published last year, Manyuan Long of the University of Chicago and his team showed that two recently evolved young insect orphans help shape foraging behaviour in the fruit fly Drosophila.

In corals, jellyfish and polyps, orphan genes guide the development of explosive stinging cells, sophisticated structures that launch toxin-filled capsules to stun prey. In the freshwater polyp Hydra, orphans guide the development of feeding tentacles around the organism's mouth. And the polar cod's orphan antifreeze gene enables it to survive life in the icy Arctic.

However improbable...

Curiously, orphan genes are often expressed in the testes - and in the brain. Lately, some have even dared speculate that orphan genes have contributed to the evolution of the biggest innovation of all, the human brain. In 2011, Long and his colleagues identified 198 orphan genes in humans, chimpanzees and orang-utans that are expressed in the prefrontal cortex, the region of the brain associated with advanced cognitive abilities. Of these, 54 were specific to humans. In evolutionary terms, the genes are young, less than 25 million years old, and their arrival seems to coincide with the expansion of this brain area in primates. "It suggests that these new genes are correlated with the evolution of the brain," says Long.

Critics argue that most genes, new or old, are somehow involved with the workings of the brain, and that correlation does not prove causation. But Long cites a recent animal study that lends credence to the theory. Expressing one of the human orphan genes, SRGAP2C, in the neurons of developing mice doesn't make the animals' brains grow bigger. But it does encourage the nerve cells to grow denser arrays of dendritic spines, the tiny protrusions that enable neurons to connect with their neighbours. Having more connections might increase computing power, he argues. So these recently evolved human genes may have helped shape the human brain. "I think we've underestimated orphan genes," says geneticist Diethard Tautz of the Max-Planck Institute for Evolutionary Biology in Plön, Germany.

But where did they come from? In 2003, Tautz and a colleague suggested that orphan genes are formed by duplication, but then evolve so rapidly that any similarity to the original is obliterated. And they did have evidence that seemed to support this idea. They showed that orphans in fruit flies evolve three times more quickly than non-orphans.

Orphan genes were thus crowbarred into the old model of genes arising by duplication. Later studies, however, suggest this can only explain the origins of a minority of orphans. So while the process is clearly important, it's not the whole story. "The idea seemed reasonable at the time," says Tautz, "because the alternative seemed so unlikely."

The alternative? The only other possibility was that genes really can evolve from scratch, from random stretches of non-coding DNA. This is the idea long dismissed as completely implausible, because the leap from non-coding DNA to a gene with a useful protein product was considered so huge as to be impossible. But nature hasn't read the textbooks. A few years ago, evidence began to emerge of genes created "de novo" in yeast, rice, mice and fruit flies. Then in 2009, David Knowles and Aoife McLysaght of the University of Dublin in Ireland showed that three orphan genes in people had indeed been created from scratch.

They found that DNA sequences nearly identical to the genes existed in several other primates but were non-coding, meaning the genes must have arisen sometime after the human-chimpanzee split. They also showed that the orphan genes are transcribed to RNA and then translated into protein in multiple tissues, though the functions of the genes are not known yet.

In 2011, another team described a further 60 human orphan genes created from scratch. McLysaght thinks this might be an overestimate - she believes that de novo gene synthesis is a rare phenomenon.

Some other researchers, however, are starting to think it may be surprisingly common. A study of 270 primate orphan genes, led by M. Mar Albà and Macarena Toll-Riera of the Municipal Foundation Institute for Medical Research in Barcelona, Spain, found that only a quarter could be explained by rapid evolution after duplication (Molecular Biology and Evolution, vol 26, p 603). Instead, around 60 per cent appeared to be new. "De novo evolution is clearly a strong force - constantly generating new genes over time," says Tautz. "It seems possible that most orphan genes have evolved through de novo evolution."

But how can it be possible? Knowles and McLysaght showed that the orphan genes they found sit next to and slightly overlap existing, older genes, so the orphans might be able to "borrow" their switches. Similarly, Albà and Toll-Riera found that half of the 270 primate orphans had acquired sequences from the genes of "transposable elements", genetic parasites that can jump around in the genome. Meanwhile, the ENCODE study of the human genome published earlier this year showed that our DNA is littered with millions of potentially useful short switching sequences, and that single switches can interact with many genes.

All this suggests that it is relatively easy for non-coding DNA to acquire the switches needed for RNA copies of it to be made. Indeed, the ENCODE study found that as much as 80 per cent of DNA is copied into RNA at least occasionally. Some argue that all this RNA is functional, but another interpretation is that most of this activity is just noise, and that junk DNA is routinely transcribed into RNA.

Proto-genes

If so, we are basically experimenting with thousands of potential new genes all the time - and Anne-Ruxandra Carvunis of the University of California, San Diego, has shown that this is indeed the case, at least in yeast. Last year, her team analysed 108,000 short, unknown but potentially protein-coding sequences in the yeast genome (Nature, vol 487, p 370). More than 1000 were interacting with the cell's protein-making factory, suggesting that they were being converted to proteins. "These may just be the tip of the iceberg," says Carvunis.

Her findings suggest that the protein-making factories in yeast are constantly churning out new proteins, allowing them to be "tested", and she suspects that same is happening in all complex organisms. In between non-coding DNA and fully fledged genes, Carvunis thinks there is a whole continuum of "proto-genes". Most will code for proteins that are neutral or harmful, so there will be no selection and the vast majority of proto-genes will revert to non-coding DNA sooner or later. But a few proto-genes that are neutral or maybe even helpful will sometimes persist, and start to gather beneficial mutations. Over millions of years of natural selection, they can become a proper gene - and thus is an orphan born.

All this helps explain why orphan genes are often expressed in the testis. In most cells, DNA is tightly packaged, which reduces the chances of RNA copies being made. In certain immature sperm cells, however, the structure is more open, making it easier for proto-genes to be copied into RNA. Over time, the gene may come to be expressed in other tissues and evolve new functions.

New discoveries about the nature of proteins also make the idea of genes arising de novo seem far more plausible. It was once thought proteins must be folded into a delicate, precise 3D structure to work properly, but it now seems many exist in a state of intrinsic disorder, flitting through thousands of different possible conformations, all the while remaining perfectly functional. About half of human proteins have at least one long intrinsically disordered segment, while 10 per cent are disordered from beginning to end.

Peter Tompa of the Flanders Institute of Biotechnology in Brussels, who studies intrinsically disordered proteins, suspects that new orphan genes are likely to code for disordered proteins because they are easier to make than folded proteins. And disordered proteins often play a role in cell signalling and regulation. "I wouldn't be surprised if orphan genes turn out to have regulatory functions," says Tompa.

Perhaps this helps explain why orphan genes can become essential very quickly. In 2010, Long's team used RNA interference to switch off evolutionarily old and new genes in fruit flies. They found that new genes, including orphans, were just as likely to be essential for life as old genes (Science, vol 330, p 1682). "This goes against the textbooks, which say the genes encoding essential functions were created in ancient times," says Long.

We still have a lot to learn about orphan genes, but we are now starting to trace their ancestry. And it looks as if we couldn't find the families of most orphans because they don't really have families. The raw DNA from which they sprung can be traced, but as genes they are the first of their kind. In this sense, the term orphans may be a misnomer. Perhaps they ought to be renamed Pinnochio genes - non-genes carved by chance and natural selection into proper, "living" genes.

http://www.newscientist.com/article/mg2 ... ?full=true
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Potential AIDS cure -- gene therapy may make HIV self-destruct
cultivate a white rose
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Azrael wrote:Potential AIDS cure -- gene therapy may make HIV self-destruct
Would be great if it panned out.
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While the tone is a bit alarmist, the next big surprise for civilization will probably come from some overlooked area . . .

The Rise of Superbugs Called 'Apocalyptic Scenario'
"We already are seeing infections that are untreatable," Spellberg said. Besides the rising threats of antibiotic-resistant tuberculosis and gonorrhea, he cited three bacterial infections of particular concern: Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumonia.

Each of these bacteria can cause a number of infectious diseases, including pneumonia, septicemia and urinary tract infections. In the case of Klebsiella, Spellberg noted, there's just one highly toxic drug left, and it's effective only about half the time it's used.

It's equally alarming that antibiotic drug development is at a virtual standstill, he said. "The pipeline is barren," partly because pharmaceutical companies have few incentives for developing antibiotics that people take for just a few days or weeks, Spellberg said.
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http://www.bbc.co.uk/news/science-environment-21150047
Quantum biology: Do weird physics effects abound in nature?
By Jason Palmer and Alex Mansfield BBC News and BBC Radio Science Unit
Perfume chemist The multi-billion-dollar fragrance industry might just benefit from the ideas in quantum biology

Disappearing in one place and reappearing in another. Being in two places at once. Communicating information seemingly faster than the speed of light.

This kind of weird behaviour is commonplace in dark, still laboratories studying the branch of physics called quantum mechanics, but what might it have to do with fresh flowers, migrating birds, and the smell of rotten eggs?

Welcome to the frontier of what is called quantum biology.

It is still a tentative, even speculative discipline, but what scientists are learning from it might just spark revolutions in the development of new drugs, computers and perfumes - or even help in the fight against cancer.

Until recently, the delicate states of matter predicted by quantum mechanics have only been accessed with the most careful experiments: isolated particles at blisteringly low temperatures or pressures approaching that of deep space.

The idea that biology - impossibly warm, wet and messy to your average physicist - should play host to these states was almost heretical.

But a few strands of evidence were bringing the idea into the mainstream, said Luca Turin of the Fleming Institute in Greece.

"There are definitely three areas that have turned out to be manifestly quantum," Dr Turin told the BBC. "These three things... have dispelled the idea that quantum mechanics had nothing to say about biology."
SEM of chloroplast Deep within plants' energy-harvesting machinery lie distinctly quantum tricks

The most established of the three is photosynthesis - the staggeringly efficient process by which plants and some bacteria build the molecules they need, using energy from sunlight. It seems to use what is called "superposition" - being seemingly in more than one place at one time.

Watch the process closely enough and it appears there are little packets of energy simultaneously "trying" all of the possible paths to get where they need to go, and then settling on the most efficient.

"Biology seems to have been able to use these subtle effects in a warm, wet environment and still maintain the [superposition]. How it does that we don't understand," Richard Cogdell of the University of Glasgow told the BBC.

But the surprise may not stop at plants - there are good hints that the trickery is present in animals, too: the navigational feats of birds that cross countries, continents or even fly pole to pole present a compelling behavioural case.

Experiments show that European robins only oriented themselves for migration under certain colours of light, and that very weak radio waves could completely mix up their sense of direction. Neither should affect the standard compass that biologists once believed birds had within their cells.

What makes more sense is the quantum effect of entanglement. Under quantum rules, no matter how far apart an "entangled" pair of particles gets, each seems to "know" what the other is up to - they can even seem to pass information to one another faster than the speed of light.

Quantum mechanics starts with the simple idea that energy does not come in just any amount; it comes in discrete chunks, called quanta. But deeper into the theory, some truly surprising - and useful - effects crop up

Superposition: A particle exists in a number of possible states or locations simultaneously - strictly, an electron might be in the tip of your finger and in the furthest corner of the Universe at the same time. It is only when we observe the particle that it 'chooses' one particular state
Entanglement: Two particles can become entangled so that their properties depend on each other - no matter how far apart they get. A measurement of one seems to affect the measurement of the other instantaneously - an idea even Einstein called "spooky"
Tunnelling: A particle can break through an energy barrier, seeming to disappear on one side of it and reappear on the other. Lots of modern electronics and imaging depends on this effect

How Einstein changed our ideas about the entire Universe

Experiments suggest this is going on within single molecules in birds' eyes, and John Morton of University College London explained that the way birds sense it could be stranger still.

"You could think about that as... a kind of 'heads-up display' like what pilots have: an image of the magnetic field... imprinted on top of the image that they see around them," he said.

The idea continues to be somewhat controversial - as is the one that your nose might be doing a bit of quantum biology.

Most smell researchers think the way that we smell has to do only with the shapes of odour molecules matching those of receptors in our noses.

But Dr Turin believes that the way smell molecules wiggle and vibrate is responsible - thanks to the quantum effect called tunnelling.

The idea holds that electrons in the receptors in our noses disappear on one side of a smell molecule and reappear on the other, leaving a little bit of energy behind in the process.

A paper published in Plos One this week shows that people can tell the difference between two molecules of identical shape but with different vibrations, suggesting that shape is not the only thing at work.

What intrigues all these researchers is how much more quantum trickery may be out there in nature.

"Are these three fields the tip of the iceberg, or is there actually no iceberg underneath?" asked Dr Turin. "We just don't know. And we won't know until we go and look."
'Hugely important'

That question has ignited a global push. In 2012, the European Science Foundation launched its Farquest programme, aiming to map out a pan-European quantum research structure in which quantum biology plays a big role.

And the US defence research agency, Darpa, has been running a nationwide quantum biology network since 2010. Departments dedicated to the topic are springing up in countries ranging from Germany to India.
European robin Do European robins use the molecular equivalent of a pilot's heads-up display?

A better understanding of smell could make the hit-and-miss business of making new fragrances more directed, and learning from nature's tricks could help with developing next-generation quantum computers.

But what the next wave of quantum biologists finds could be truly profound.

Simon Gane, a researcher at the Royal National Throat, Nose and Ear Hospital and lead author of the Plos One paper, said that the tiny receptors in our noses are what are called G-protein coupled receptors.

"They're a sub-family of the receptors we have on all cells in our body - they're the targets of most drug development," he explained.

"What if - and this is a very big if - there's a major form of receptor-drug interaction that we're just not noticing because we're not looking for a quantum effect? That would have profound implications for drug development, design and discovery."

Jim Al-Khalili of the University of Surrey is investigating whether tunnelling occurs during mutations to our DNA - a question that may be relevant to the evolution of life itself, or cancer research.

He told the BBC: "If quantum tunnelling is an important mechanism in mutations, is quantum mechanics going to somehow answer some of the questions about how a cell becomes cancerous?

"And suddenly you think, 'Wow!' Quantum mechanics is not just a crazy side issue or a fringe field where some people are looking at some cranky ideas. If it really might help answer some of the very big questions in science, then it's hugely important."
"I fancied myself as some kind of god....It is a sort of disease when you consider yourself some kind of god, the creator of everything, but I feel comfortable about it now since I began to live it out.” -- George Soros
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