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Contents contributed and discussions participated by grayton downing

grayton downing

Darwin Still Rules, but Some Biologists Dream of a Paradigm Shift - New York Times - 1 views

  • Paradigm shifts are the stuff of scientific revolutions. They change how we view the world, the sorts of questions that scientists consider worth asking, and even how we do science.
  • Many scientists suffer from a kind of split personality. We believe that this is the most exciting time to be working while yearning for the excitement of a revolution. What ambitious scientist would not want to be part of a paradigm shift? Not surprisingly, this yearning occasionally manifests itself in proclamations that a revolution is at hand.
  • Comparative studies of development have illuminated how genes operate, and evolve, and this places less emphasis on the gradual accumulation of small genetic changes emphasized by the modern synthesis. Work in ecology has emphasized the role organisms play in building their own environments, and studies of the fossil record raise questions about the role of competition.
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  • One advantage developmental biologists have over paleontologists is that they can experiment on the development of these animals.
  • The failure to consider how biodiversity grows reflects an even more troubling flaw in the modern synthesis: it lacks any real sense of history.
grayton downing

Wonder Woman Shouldn't Be a Sidekick - Noah Berlatsky - The Atlantic - 0 views

  • for example, the main story is about Superman needing to accept and embrace his awesomeness; Wonder Woman is mostly there to advise and comfort and tell him his values are great before giving him the kiss that awakens him to his destiny
  • especially frustrating because, initially, the whole point of Wonder Woman was that the world needed her and not Superman.
  • was a psychologist and a committed feminist, and he conceived Wonder Woman as a superior replacement for the Man of Steel. In a 1944 article for The American Scholar, he noted that, "Superman and his innumerable followers satisfy the universal human longing to be stronger than all opposing obstacles."  He added that "the wish to be super-strong is a healthy wish, a vital, compelling, power-producing desire."
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  • Marston's Wonder Woman didn't spend her time encouraging Superman to be awesome, because she was way to busy being awesome herself.
  • blood-curdling masculinity. A male hero
  • But the underlying message you get when you watch Wonder Woman defer over and over to Superman's awesomeness is that the most important person in the world has to be a man.
grayton downing

Are You a Workaholic? Blame Your Parents - Lauren Davidson - The Atlantic - 0 views

  • Career-oriented adults—your typical “workaholic”—value the social status and prestige that comes with professional achievement, and derive much of their identity from their jobs.
  • not a straightforward transfer of values. People who perceive their father to have a strong career-orientation are more likely to be career-oriented themselves—but career-determined mothers have no effect on their kids’ work orientation
  • do have a notable effect on whether children have a job-orientation mentality. Adolescents who are close to their mothers are less likely to view work as just a job when they grow up, probably because they’ve been raised to value social, rather than instrumental, life experiences.
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  • both parents display the same work ethic has an amplified influence, but only in the case of calling-oriented offspring. As our capitalist society favors money and professional achievement, a child with two calling-oriented parents is more likely to have the confidence to ignore these societal pressures and pursue her dreams.
  • Children can affect their parents’ work ethic, too. Allowing people to bring their children into the office has been shown to boost efficiency and productivity—and could help raise that next generation of career-oriented workers.
grayton downing

So What If Everyone at Harvard Gets an A? - Eleanor Barkhorn - The Atlantic - 1 views

  • Yesterday, we ran a story about a rather astonishing fact that the Harvard Crimson uncovered: The most common grade at Harvard is an A.
  • Kids these days—especially high-achieving kids who end up at elite colleges—are so conditioned to expect praise that they fall apart when they face failure.
  • patting its students on the head rather than truly challenging them. "Everyone gets a trophy," Ryan Foster tweeted in response to the story. "Everyone is special!,
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  • Come meet our students, & you will not be surprised—(or resentful)—that they receive high grades. Possibly, you will be impressed.
  • "Grade inflation" a code term like "affirmative action."
  • These students should be A's. 
  • At large universities where thousands are admitted, bell-curve grading is used to "flunk out" many freshmen. Very different in Ivy League. Bell-curve grading, which assures a percent of low grades & failures, is a cruel academic necessity in some quarters. Encourages cheating.  
  • And while I did find most of my classmates to be "excellent"—that is: smart, compassionate, well-read, curious—a lot of us weren't especially hard-working.
  • saw our time at Princeton as a reward, not an opportunity to push ourselves again, even harder. The university's relatively lax grading policies only encouraged that mentality.
  • Starting my junior fall, professors could give out only a limited number of A-range grades. The change prompted lots of anxiety and indignation from the student body—and now, nine years later, it may be rolled back. But for me, "grade deflation" was a much-needed kick in the pants. I started reading more carefully, taking more diligent notes, developing relationships with my professors and their teaching assistants. I ended up learning a lot more
  • Yes, hard-working students should be rewarded with good grades. But a very good way to inspire students to work hard in the first place is to make good grades worth something.
grayton downing

The Hospital Is No Place for the Elderly - Jonathan Rauch - The Atlantic - 0 views

  • The patient is feeble and near death, his bone marrow eviscerated by cancer. The supervising oncologist has ordered a course of chemotherapy using a very toxic investigational drug. Stuart knows enough to feel certain that the treatment will kill the patient, and he does not believe the patient understands this.
  • “I walked out of that room and said, ‘There has got to be a better way than this,’ ” he told me recently. “I was appalled by how we care for—or, more accurately, fail to care about—people who are near the end of life. We literally treat them to death.”
  • advocating home-based primary care, which represents a fundamental change in the way we care for people who are chronically very ill. The idea is simple: rather than wait until people get sick and need hospitalization, you build a multidisciplinary team that visits them at home,
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  • late-life care for the chronically sick is not only expensive but also, much too often, ineffective and inhumane. For years, the system seemed impervious to change.
  • Thanks to modern treatment, people commonly live into their 70s and 80s and even 90s, many of them with multiple chronic ailments.
  • five or more chronic conditions account for less than a fourth of Medicare’s beneficiaries but more than two-thirds of its spending—and they are the fastest-growing segment of the Medicare population. What to do with this burgeoning population of the frail elderly?
  • “On average, Medicare spends $20,870 per beneficiary who dies while in the hospital.”
  • Home-based primary care comes in many varieties, but they share a treatment model and a business model. The treatment model begins from the counterintuitive premise that health care should not always be medical care.
  • by keeping patients out of the hospital whenever possible, saves Medicare upwards of $2,000 a month on each patient, maybe more
  • program collects whatever payment it can from Medicare and private insurance, it operates at a loss, and is run as a community service and a form of R&D.
  • Under the new health-care law, Medicare has begun using its financial clout to penalize hospitals that frequently readmit patients. Suddenly, hospitals are not so eager to see Grandma return for the third, fourth, or fifth time.
  • home-based model of primary care will be a challenge.
  • That would be like spiritual suicide right now,” he told me, “because there is so much going on. I’m more hopeful all the time. We’ve rolled the rock all the way to the top of the hill, and now we have to run to keep up as it rolls down the other side.”
grayton downing

Origin of Domestic Dogs | The Scientist Magazine® - 0 views

  • Domestic dogs evolved from a group of wolves that came into contact with European hunter-gatherers between 18,800 and 32,100 years ago and may have since died out.
  • ompared the genes of a wide variety of living dogs and wolves, but modern samples can be deceptive. Dogs and wolves diverged so recently that many of their genes have not had time to separate into distinct lineages. They have also repeatedly hybridized with each other, further confusing their genealogies.
  • “This suggests that the population of wolves in Europe that gave rise to modern dogs may have gone extinct, which is plausible given how humans have wiped out wolves over the centuries
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  • “It would be a mistake to jump and say that dogs were domesticated in Europe and not anywhere else,” he said. “We know pigs were domesticated independently in China and Turkey, so there’s no thinking that dog domestication had to happen in just one place.”
grayton downing

BBC News - Y chromosome: Why men contribute so little - 0 views

  • "The Y chromosome is a symbol of maleness," lead researcher Professor Monika Ward told the BBC.
  • "may be possible to eliminate the Y chromosome" if the role of these genes could be reproduced in a different way, but added a world without men would be "crazy" and "science fiction".
  • "But on a practical level it shows that after large deletions of the Y chromosome it is still possible to reproduce, which potentially gives hope to men with these large deletions,
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  • "The experiments are elegant and seem to show that in the mouse sperm production can be achieved when only two genes from the Y-chromosomes are present.
  • "Whilst this is of limited use in understanding human fertility, this kind of work is important if we are to unravel to complexities of how genes control fertility."
grayton downing

Males Court Bearded Ladies Less | The Scientist Magazine® - 0 views

  • many females also don blue ornamentations like the males, though they are less bright. These so-called “bearded ladies”—masculinized females—suffer reproductive consequences as a result of their markings.
  • We were very excited to find that ornamented females appear to pay costs of reduced reproductive output,
  • Ornamented females seemed less popular in the lab, as well: males spent less time courting them.
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  • males dislike ornamented females because blue badges indicate a potentially negative quality in females. Although both sexes may develop similar ornaments because they share the genes that underlie the phenotype, expressing the ornament can be beneficial in one sex but detrimental in another.
  • One solution is to have the expression of [ornamentation] regulated by other factors that are already different between sexes,”
  • the causation and persistence of ornamentation in females” as well as “unambiguous information on fitness consequences of female ornamentation,” he continued. Because both sexes produce testosterone, added Cox, “regulation by testosterone is not a perfect mechanism for complete sex-limitation [of blue badge expression].”
  • detrimental ornamentation in females is a paradox that “begs the interesting question of why male-typical ornamentation persists in female fence lizards,” said Langkilde. “We plan to follow this up by examining potential benefits associated with these male-typical ornaments in females.”
grayton downing

Newborn Immune Systems Suppressed | The Scientist Magazine® - 0 views

  • sterile world of the womb, at birth babies are thrust into an environment full of bacteria, viruses, and parasites. They are very vulnerable to these infections for their first months of life—a trait that has long been blamed on their immature immune systems.
  • “This more intricate regulation of immune responses makes more sense than immaturity,” said Sing Sing Way, who led the study, “because it allows a protective response to be mounted if needed.” This may explain why newborn immune responses, though generally weak, also vary wildly between different babies and across different studies.
  • njecting 6-day-old mice with splenocytes (a type of white blood cell) from adults. Newborn mice are normally 1,000 times more suspectible to bacterial infections than adults, but despite receiving working immune cells, they became no less vulnerable.
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  • Way added that there might be other reasons why newborns should carry immunosuppressive cells
  • Baby formulas contain small amounts of arginine. Sidney Morris, a biochemist from the University of Pittsburgh, said that it may be important to avoid fortifying them with extra arginine, lest it swamps the arginase activity of CD71+ cells, releases the immune system, and causes problems for the developing infants’ guts.
  • “Whether the precise mechanism of immunosuppression is the same or different in each of these circumstances remains to be determined,” he said.
grayton downing

How the Brain Creates Personality: A New Theory - Stephen M. Kosslyn and G. Wayne Mille... - 0 views

  • It is possible to examine any object—including a brain—at different levels
  • if we want to know how the brain gives rise to thoughts, feelings, and behaviors, we want to focus on the bigger picture of how its structure allows it to store and process information—the architecture, as it were. To understand the brain at this level, we don’t have to know everything about the individual connections among brain cells or about any other biochemical process.
  • top parts and the bottom parts of the brain have differ­ent functions. The top brain formulates and executes plans (which often involve deciding where to move objects or how to move the body in space), whereas the bottom brain classifies and interprets incoming information about the world. The two halves always work together;
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  • You have probably heard of this theory, in which the left and right halves of the brain are characterized, respectively, as logical versus intuitive, verbal versus perceptual, analytic versus synthetic, and so forth. The trouble is that none of these sweeping generalizations has stood up to careful scientific scrutiny. The dif­ferences between the left and right sides of the brain are nuanced, and simple, sweeping dichotomies do not in fact explain how the two sides function.
  • top and bottom portions of the brain have very different functions. This fact was first discovered in the context of visual perception, and it was supported in 1982 in a landmark report by National Medal of Science winner Mortimer Mishkin and Leslie G. Ungerleider, of the National Institute of Mental Health.
  • scientists trained monkeys to perform two tasks. In the first task, the monkeys had to learn to recognize which of two shapes concealed a bit of food.
  • These functions occur relatively close to where neural connec­tions deliver inputs from the eyes and ears—but processing doesn’t just stop there.
  • top parts of our frontal lobe can take into account the confluence of information about “what’s out there,” our emo­tional reactions to it, and our goals.
  • Four distinct cognitive modes emerge from how the top-brain and bottom-brain systems can interac
  • The two systems always work together. You use the top brain to decide to walk over to talk to your friend only after you know who she is (courtesy of the bottom brain). And after talking to her, you formulate another plan, to enter the date and time in your calendar, and then you need to monitor what hap­pens (again using the bottom brain) as you try to carry out this plan (a top-brain activity).
  • speak of differences in the degree to which a person relies on the top-brain and bottom-brain systems, we are speaking of differences in this second kind of utilization, in the kind of processing that’s not simply dictated by a given situation. In this sense, you can rely on one or the other brain system to a greater or lesser degree.
  • The degree to which you tend to use each system will affect your thoughts, feel­ings, and behavior in profound ways. The notion that each system can be more or less highly utilized, in this sense is the foundation of the Theory of Cognitive Modes. 
grayton downing

The Stereotypes About Math That Hold Americans Back - Jo Boaler - The Atlantic - 2 views

  • Mathematics education in the United States is broken. Open any newspaper and stories of math failure shout from the pages: low international rankings, widespread innumeracy in the general population, declines in math majors. Here’s the most shocking statistic I have read in recent years: 60 percent of the 13 million two-year college students in the U.S. are currently placed into remedial math courses; 75 percent of them fail or drop the courses and leave college with no degree.
  • We need to change the way we teach math in the U.S., and it is for this reason that I support the move to Common Core mathematics.
  • One of the reasons for these results is that mathematical problems that need thought, connection making, and even creativity are more engaging for students of all levels and for students of different genders, races, and socio-economic groups. This is not only shown by my research but by decades of research in our field.
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  • ways of working are critical in mathematical work and when they are taught and valued, many more students contribute, leading to higher achievement
  • mathematics education we suffer from the widespread, distinctly American idea that only some people can be “math people.” This idea has been disproved by scientific research showing the incredible potential of the brain to grow and adapt. But the idea that math is hard, uninteresting, and accessible only to “nerds” persists. 
  • harsh stereotypical thinking—mathematics is for select racial groups and men. This thinking, as well as the teaching practices that go with it, have provided the perfect conditions for the creation of a math underclass.
  • online platform explaining research evidence on ability and the brain and on good mathematics teaching, for teachers and parents. The course had a transformative effect. It was taken by 40,000 people, and 95 percent said they would change their teaching or parenting as a result.
  • does not simply test a mathematical definition, as the first does. It requires that students visualize a triangle, use transformational geometry, consider whether different cases satisfy the mathematical definition, and then justify their thinking.
  • There is a good reason for this: Justification and reasoning are two of the acts that lie at the heart of mathematics. They are, in many ways, the essence of what mathematics is.  Scientists work to prove or disprove new theories by finding many cases that work or counter-examples that do not. Mathematicians, by contrast prove the validity of their propositions through justification and reasoning.
  • The young people who are successful in today’s workforce are those who can discuss and reason about productive mathematical pathways, and who can be wrong, but can trace back to errors and work to correct them.
  • American idea that those who are good at math are those who are fast. Speed is revered in math classes across the U.S., and students as young as five years old are given timed tests—even though these have been shown to create math anxiety in young children. Parents use flash cards and other devices to promote speed, not knowing that they are probably damaging their children’s mathematical development
  • The fact of being quick or slow isn't really relevant
  • gives more time for depth and exploration than the curricula it has replaced by removing some of the redundant methods students will never need or use.
grayton downing

The Epigenetics of Drug Abuse | The Scientist Magazine® - 0 views

  • Medicine at Mount Sinai and her colleagues found significant changes in gene networks related to glutamate pathways in the striatum, an area commonly linked to drug use
  • “In heroin users, there are clear disturbances of epigenetic mechanisms that directly correlate with their years of drug use,”
  • the researchers found evidence of alterations to DNA’s structure, including its chromatin, to produce repeatable, predictable changes in gene expression. “It’s well established that cocaine addiction has lasting effects on the brain,” Nestler said in a press release. “But studies in our lab begin to reveal just how extensive these changes are and how they might change brain function. This level of understanding could lead to better treatments for addiction.”
grayton downing

Opinion: I Want My Kidney | The Scientist Magazine® - 0 views

  • Indeed,10 years ago, one of Atala's young patients, Luke Massella, received an engineered bladder made using similar technology.
  • human kidney, albeit non-functional, takes us a step closer to utilizing the enormous potential of stem cells from different sources.
  • disorders can contribute to end-stage renal disease, which is the main indicator for kidney transplantation. Diabetes alone, which is on the rise the world over, is the major cause, responsible for more than 40 percent of all end-stage renal disease cases in need of kidney transplant
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  • Research on differentiated kidney cells, particularly podocytes that can be cultured in the lab, may hold some answers. Although there are a few human- and mouse-derived cell lines that potentially differentiate into functional podocytes, there is a need for better cell lines and systems that mimic the in vivo situation more closely
grayton downing

Retracing Steps | The Scientist Magazine® - 1 views

  • growing body of research has highlighted scientists’ inability to reproduce one another’s results, including a 2012 study that found only 11 percent of “landmark” cancer studies investigated could be independently confirmed.
  • “Some communities have standards requiring raw data to be deposited at or before publication, but the computer code is generally not made available, typically due to the time it takes to prepare it for release,”
  • Sage’s solution? An open-source computational platform, called Synapse, which enables seamless collaboration among geographically dispersed scientific teams—providing them with the tools to share data, source code, and analysis methods on specific research projects or on any of the 10,000 datasets in the organization’s massive data corpus. Key to these collaborations are tools embedded in Synapse that allow for everything from data “freezing” and versioning controls to graphical provenance records—delineating who did what to which dataset, for example.
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  • It was indeed the connecting data framework that held the entire project together,” said Josh Stuart, professor of biomolecular engineering at the University of California, Santa Cruz, who is part of the TCGA-led project.
  • “It provides a framework for the science to be extended upon, instead of publication as a finite endpoint for research,”
grayton downing

2013 Life Sciences Salary Survey | The Scientist Magazine® - 0 views

  • US researchers across academia, industry, and government earn an average of nearly $96,000 per year in total compensation, including base salary, bonuses, and other income, compared with a European average of just $66,700. Life scientists in Canada come in right in the middle, at $78,200, while researchers in India lag far behind, earning an average of just $11,200.
  • life sciences, could explain the oft-cited “brain drain,” which has seen foreign researchers flock to the U.S. in search of good jobs with ample compensation.
  • Across the globe, scientists earn a wide range of salaries, with US researchers earning nearly $96,000 total compensation per year while India lags far behind at less than $11,200, though this discrepancy is at least partly explained by the vast differences in cost of living in the two countries. Still, this enormous gulf is a strong driver of “brain drain
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  • Dramatic budget cuts in the past few years, however, may make US academia less of a paradise.
  • European salaries also lag behind those in the U.S., with the average European life scientist making anywhere from 41 to 82 percent of what the average American researcher earns.
  • Europe make around 50 percent of what full professors there make, postdocs in the U.S. earn less than a third of a professor’s salary.
  • Equal Pay Act prohibited unequal pay for men and women doing the same jobs. But salary disparities remain, including in the life sciences. “It is a persistent problem,” says Curtis. “It’s important for people to realize that there are continuing inequalities.” In this year’s survey, for example, male respondents in the U.S. reported an average total income of around $111,000 per year, while their female counterparts averaged just $77,000 in annual pay.
  • fewer women make it to high-level positions than men do, says Curtis.
  • life-science specialty is often tomorrow’s overcrowded field. Case in point: genomics versus genetics. Genomics relies heavily on bioinformatics, mathematics, and computational modeling
  • survey highlights the well-established discrepancy between industry and academic salaries. According to the data, life scientists in industry make around $136,000 per year, compared to average academic earnings of $85,000.
grayton downing

Genetic Diversity in the Brain | The Scientist Magazine® - 0 views

  • Genomic analyses of single human neurons—either from postmortem brains or those derived in culture—reveal a considerable degree of DNA copy number variation, according to a paper
  • likely that these genetic differences affect brain cell function, and they may even shape our personalities, academic abilities, and susceptibilities to neurological diseases.
  • There was a really long-standing hypothesis that given the huge diversity of cell types in the brain, there might be [genetic] mechanisms . . . to generate [the] diversity,” Hall explained.
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  • found similar copy number variations in neurons derived in culture from human induced pluripotent stem cells (iPSCs)
  • neural progenitor cells derived from the same iPSC lines did not exhibit such abundant diversity. This suggested that the genetic variation in neurons occurred only at later stages of differentiation. And that the variation developed in a short space of time—the seven weeks it took to differentiate neurons from neural progenitors. Furthermore, the results implied that genetic variations seen in adult postmortem brains were unlikely to be a mere side effect of aging.
grayton downing

Tuning the Brain | The Scientist Magazine® - 0 views

  • first neurosurgeries took place about 7,000 years ago in South America with the boring of holes into hapless patients’ skulls, a process known as trephination. Practitioners of the day believed the source of neurologic and psychiatric disease to be evil spirits inhabiting the brain, and the way to treat such disorders, they reasoned, was to make holes in the skull and let the evil spirits escape. The procedure was surprisingly common, with as many as 1 percent of skulls at some archaeological sites having these holes.
  • disorders is a consequence of pathological activity within a specific brain circuit. In Parkinson’s disease and dystonia, neurons in the motor circuits misfire, causing aberrant movements of the limbs and torso. Malfunction in circuits that regulate mood can lead to depression.
  • observing patients’ behavioral changes following the stimulation or inhibition of specific neural circuits, DBS is helping to explain what goes wrong in the brain to cause symptoms
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  • addition to neuroimaging techniques that can reveal regional brain activity, brain lesioning can also help shed light on the most important targets for a particular disorder. In brain lesioning, misfiring neurons or their connections are destroyed, most commonly using a heating probe inserted in the brain. Once the first patients are treated, data on effectiveness and side effects, in combination with continued neuroimaging, can help further focus the targets. Lesioning is an alternative to DBS in certain specific cases and can be effective, but it is irreversible, and any untoward effects can be permanent. Because the dose of DBS at the same site can be adjusted down if adverse effects emerge, it is considered to be a potentially safer alternative.
grayton downing

Drug Widens Immunity to Flu | The Scientist Magazine® - 0 views

  • drug rapamycin paradoxically helped to protect mice against a diverse range of influenza viruses after the animals were vaccinated against just one flu strain.
  • many subtypes and strains of influenza, which evolve at great speed and often hybridize into entirely new strains. Current flu vaccines cannot protect against all of these strains, which forces scientists to try and predict those most likely to cause problems in the coming year.
  • In treated mice, the B cells produced a more diverse repertoire of antibodies, which targeted different parts of the incoming viruses, including regions that are conserved across many strains. This provided protection against flu viruses regardless of strain. 
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  • cross-reactive antibodies bind relatively weakly to their targets and, under normal circumstances, would probably get outcompeted by antibodies with a narrower focus but higher affinity. “For whatever reason, antibodies to the conserved regions are very rare,”
  • possible to skew the response towards more broadly cross-reactive antibodies, in mice, in a particular situation,”
  • not advocating that we use rapamycin [in humans],” said McGargill. However, her group’s discovery could point to other ways of achieving the same effect, perhaps by manipulating the immune system into producing more cross-reactive antibodies. “Maybe instead of trying to enhance the immune response, we need to dampen it a little bit, and allow it to be more diverse,
grayton downing

Post-Publication Peer Review Mainstreamed | The Scientist Magazine® - 0 views

  • peer review. The process has been blamed for everything from slowing down the communication of new discoveries to introducing woeful biases to the literature
  • organized post-publication peer review system could help “clarify experiments, suggest avenues for follow-up work and even catch errors.” If used by a critical mass of scientists, he added, “it could strengthen the scientific process.”  
  • peer review does not elevate the quality of published science and that many published research findings are later shown to be false. In response, a growing number of scientists are working to impose a new vision of the scientific process through post-publication review,
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  • allowing for an
  • onymous comments, PubPeer aims to create an open, debate-friendly environment, while maintaining the rigor the closed review process currently used by most journals. Its creators, who describe themselves as “early-stage scientists,” have also decided to remain anonymous, citing career concerns.
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