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Posts Tagged ‘microbiology

“I do not mind if you think slowly. But I do object when you publish more quickly than you think.”*…

 

open access

 

Each year, governments around the world pour vast sums of public money into scientific research — as much as $156 billion in the United States alone. Scientists then use that funding to further human understanding of the world, and occasionally to make compelling discoveries about everything from whale brains to dwarf stars to the genetic underpinnings of deadly cancers. But often, this research — despite being subsidized with taxpayer money — ends up being published in exclusive journals that sit behind steep paywalls with three- and four-figure subscription fees, accessible to only a tiny fraction of the public.

The power of these scientific publishers — with names even lay readers might recognize: Springer Nature, Taylor & Francis, Elsevier, among a handful of others — is substantial. According to one estimate, just four corporations now publish close to 50 percent of scientific papers. Together, they control the copyright to much of the world’s scientific literature, charging billions of dollars each year for access to that body of knowledge — and securing hefty profits in the process.

Critics have argued for decades that this system is wasteful, and that the public should have access to the scientific literature that its tax dollars support. Scientists, scholars, and public institutions, they say — and not the private sector — should control access to this trove of knowledge. “The commercial interests of publishers trying to promote their brand should not be what determines what kind of scientific discipline becomes well-funded and well populated,” said Michael Eisen, a biologist at the University of California, Berkeley and a vocal supporter of the alternative model of research distribution, broadly referred to as “open-access” publishing, which has long aimed to harness the internet to make research more widely available — at little to no cost. The current system, he said, gives a handful of publishers “a disproportionate power to shape the way that science is done.”

The ensuing decades have been, in certain respects, a triumph for supporters of open access. Research funders in the United States and Europe adopted policies to make more of the research they fund accessible to the public. Several open-access organizations now operate thriving journals, and pirating tools like Sci-Hub have made it easier than ever to sneak around publishers’ paywalls.

Meanwhile, a group of Europe’s largest scientific backers — including the funding agencies of France, Britain, and the European Union as a whole — will soon require all research they underwrite to be openly accessible to everyone. That scheme, called Plan S, may be the most ambitious government-sponsored open-access effort yet — though federal officials in the U.S. are considering a policy that would require immediate open-access publishing for all federally-funded research as well, potentially revolutionizing the publishing industry. “Open Access Is Going Mainstream,” The Chronicle of Higher Education announced in a headline last year.

These successes, though, have also revealed divisions within the open-access community over two now-familiar questions: Who should run the publishing houses? And who should pay for the whole system? Instead of an open-access commons run by scholars in the public interest, the new open-access revolution increasingly looks like it will depend on the same big commercial publishers, who, rather than charging subscription prices to readers, are now flipping the model and charging researchers a fee to publish their work. The result is a kind of commercial open-access — a model very different than what many open-access activists envisioned…

As it stands, all trends point to an open-access future. The question now is what kind of open-access model it will be — and what that future may mean for the way new science gets evaluated, published, and shared. “We don’t know why we should accept that open access is a market,” said Dominique Babini, the open-access adviser to the Latin American Council of Social Sciences and a prominent critic of commercial open-access models. “If knowledge is a human right, why can’t we manage it as a commons, in collaborative ways managed by the academic community, not by for-profit initiatives?”

Peer review, editorial prep: how should we manage–and pay for– the quality control that makes scientific discourse most effective? “A Revolution in Science Publishing, or Business as Usual?

(Coronavirus has led to an explosion of scientific publication… and it has amplified the debate over open access and how to accomplish it.)

* Wolfgang Pauli

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As we share and share alike, we might send healing birthday greetings to Hattie Elizabeth Alexander; she was born on this date in 1901.  A pediatrician, microbiologist, and educator, she won international acclaim for developing a serum to combat influenzal meningitis, a common childhood disease that is nearly always fatal to infants and young children, virtually eliminating the mortality rate.

When the advent of antibiotics made the antiserum obsolete, she quickly mastered their use against all the bacterial meningitides.  Late in her career–the 1950s and 60s–she became a pioneer in microbial genetics.  She pioneered the study of bacterial mutation and resistance to antibiotics, and in 1964, she became one of the first women to head a national medical association as president of the American Pediatric Society.

Over her career she published over 70 papers.

Hattie Alexander source

 

 

“Such is the essential mystery”*…

 

For about a billion years, life on earth was a relatively simple proposition: it was composed entirely of single-celled organisms (prokaryotes) in either the bacteria or archaea families.  Then, about 2.1 billion years ago, one of those single-celled critters crawled inside another; the two merged, and a new kind of life– multi-cellular (eukaryotic) life– was born…

This inner cell—a bacterium—abandoned its free-living existence and eventually transformed into mitochondria. These internal power plants provided the host cell with a bonanza of energy, allowing it to evolve in new directions that other prokaryotes could never reach.

If this story is true, and there are still those who doubt it, then all eukaryotes—every flower and fungus, spider and sparrow, man and woman—descended from a sudden and breathtakingly improbable merger between two microbes. They were our great-great-great-great-…-great-grandparents, and by becoming one, they laid the groundwork for the life forms that seem to make our planet so special. The world as we see it (and the fact that we see it at all; eyes are a eukaryotic invention) was irrevocably changed by that fateful union—a union so unlikely that it very well might not have happened at all, leaving our world forever dominated by microbes, never to welcome sophisticated and amazing life like trees, mushrooms, caterpillars, and us.

Read the extraordinary story of how one freakish event may well account for all sophisticated life on earth in “The unique merger that made You (and Ewe, and Yew).”

* Lao Tzu

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As we fill out our family trees, we might send microscopic birthday greetings to Carl Woese; he was born on this date in 1928.  A microbiologist, Woese recognized and defined (in 1977) the existence of archaea as a third domain of life, distinct from the two previously-recognized domains, bacteria and “life other than bacteria” (eukaryotes).  The discovery revolutionized the understanding of the “family tree” of life.  And the technique he used to make it– phylogenetic taxonomy of 16S ribosomal RNA— revolutionized the practice of microbiology.

 source

 

Written by LW

July 15, 2014 at 1:01 am

Getting small…

 

First Place: a colonial plankton organism, Chaetoceros debilis (marine diatom), magnified 250x
by Wim van Egmond, of the Micropolitan Museum, Berkel en Rodenrijs, Zuid Holland, Netherland

Nikon has announced the winners of this year’s Small World Photomicrography Competition.  Browse the gallery here or here.

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As we resolve to be more thorough as we vacuum, we might send microscopic birthday greetings to Rita Rossi Colwell; she was born on this date in 1934.  The first U.S. scientist to create a computer program to analyze data related to the taxonomic classification of different strains of bacteria, she enabled the surprising discovery that the strain of cholera bacteria that had been linked to the disease belonged to the same species as benign strains of cholera. Subsequently, her team of researchers found that both the harmless and the disease-causing (toxin-producing) strains were found commonly in estuaries and coastal waters.

She is perhaps better known as the 11th Director of the National Science Foundation– the first woman to hold that post.  In 2004, she was awarded the National Medal of Science.

 source

 

Written by LW

November 23, 2013 at 1:01 am

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