NYTimes and CauseScience discuss #ASAPbio -preprints in biology

The New York Times features an article today about ASAPbio (previous blog posts about ASAPbio). The purpose of the meeting was to accelerate the usage of preprints in biology. This comes in efforts to rescue the biomedical research system from its numerous flaws- including the difficulty in publishing (previous posts on the issues in academic publishing).

ASAPbio brought together numerous biologists- including Nobel Laureates, senior PIs, journal editors, junior faculty, and postdocs (including me!)- to try and establish a system in biology to publish in an open-access, quick manner online to supplement the current publishing system.

Check out the full NYTimes article. Here are some highlights:

On Feb. 29, Carol Greider of Johns Hopkins University became the third Nobel Prize laureate biologist in a month to do something long considered taboo among biomedical researchers: She posted a report of her recent discoveries to a publicly accessible website, bioRxiv, before submitting it to a scholarly journal to review for “official’’ publication.

Why use preprints at all? One of the major issues with the current publishing system:

Unlike physicists, for whom preprints became a default method of communicating discoveries in the 1990s, biomedical researchers typically wait more than six months to disseminate their work while they submit it — on an exclusive basis — to the most prestigious journal they think might accept it for publication. If, as is often the case, it is rejected, they try another journal. As a result, it can sometimes take years to publish a paper, which is then typically available for a time only to colleagues at major academic institutions whose libraries pay for subscriptions. And because science is in many ways a relay, with one scientist building on the published work of another, the communication delays almost certainly slow scientific progress. .

One of the benefits of preprints is that the work can be featured immediately without waiting year(s) to go through peer review publication process. Another benefit is that this work is open access, which is a huge problem internationally, especially in developing countries (previous posts on open access).

Unfortunately, some journals and scientists don’t support the idea of preprints. One potential issue is that work will get “scooped” (although, physics has been doing preprints for 20+yrs and has not had this issue):

Some journal editors say that preprints would be detrimental to science. Emilie Marcus, the editor of Cell, told scientists at the #ASAPbio conference that in conversations with more than 100 scientists Cell editors had found that the main reason they wanted to use preprints was to scoop competitors, which she suggested would cause the quality of papers to decline as everyone rushed to post first: “Is that the direction that we want to go?’’ Others have argued on Twitter that allowing research to reach the public without being reviewed before publication would be irresponsible.

Preprint advocates counter that scientists care too much about their reputations to publish shoddy work, and posts to bioRxiv are clearly marked to indicate that they may contain information that “has not yet been accepted or endorsed in any way by the scientific or medical community.’’ Others note that plenty of peer-reviewed papers in high-profile journals have proved to be wrong, and some argue that carrying out peer review after a paper is published would provide a more rigorous and fair vetting of papers, anyway.

There are lots of major flaws in the current system of publishing (as it stands, scientists have to pay to submit their work to journals, that work is then reviewed FOR FREE by other scientists, and after the paper is accepted, you must pay to access it. WTF). The aim of ASAPbio is not to totally overhaul the publishing system, but to take a step in fixing the issues. If work is a) open access and b) accessible to the public on a quicker timeline, this will advance science in a huge way. Personally, if this system is to work, I believe two main things must happen:

  1. Journals must be on board. If something is posted as a preprint, journals should still accept this work for peer review and potential publication. A preprint should also act somewhat as a “timestamp” so that the work cannot get scooped. And if it does, journals should still publish the work
  2. Funding agencies should accept that preprints count as legit indicators of scientific progress. Sure, it’s not peer reviewed, but this work should show scientific productivity. Sometimes it takes years for work to get published with nothing to show for it in the meantime. This is a nice way to overcome that hurdle.

It’s nice to see several senior scientists on board!

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Anti-science Republican candidates silent on climate agreement #COP21 #science

There is a terrific editorial in the New York Times on the blaring silence from Republican presidential candidates following the historic Paris climate agreement. Turns out that science and 195 nations are hard to argue with… especially when you are arguing with lies, deceit, and fiction. Someone should tell Rep Lamar Smith and the House Committee on Science, Space, and Technology to take note.

In the past, these Republican candidates have disparaged the idea of global warming. “We’re not going to make America a harder place to create jobs in order to pursue policies that will do absolutely nothing, nothing, to change our climate,” Marco Rubio said in a Republican debate in September.

Donald Trump uttered this marvel: “I am not a believer, and I will, unless somebody can prove something to me, I believe there’s weather. I believe there’s change, and I believe it goes up and it goes down, and it goes up again.”

Ted Cruz, who seems enthralled with the idea of a climate-science conspiracy, said last week, “Climate change is the perfect pseudoscientific theory for a big-government politician who wants more power.” On Saturday, Mr. Cruz had nothing to say.

Let’s hope the candidates’ new silence suggests that they see that when 195 nations together recognize the need for immediate action, their arguments to do nothing seem more misguided than ever.

Not up for debate: The science behind vaccines

As a follow up to our Anti-Quotable post on the vaccination topic during the GOP debate, here are a few more facts on the science behind vaccination courtesy of Aaron E. Carroll in the New York Times:

  • Vaccines aren’t linked to autism.

  • The number of vaccines children receive is not more concerning than it used to be.

  • Delaying their administration provides no benefit, while leaving children at risk.

  • All the childhood vaccines are important.

The entire article does a good job summarizing current research in the field of vaccines and discrediting the comments from the GOP debate.  The final message?

All of the vaccines save lives.

It would be better for our vaccination policy for this not even to be a topic for debate, certainly not by those who aren’t immersed in the science of vaccines.

Debating any of these facts does no one any good.

Oliver Sacks – The Man Who Turned Life Into Magic – @MGleiser @npr13point7

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Be sure to read this beautiful piece by Marcelo Gleiser praising the work of neurologist, writer, and chemist Oliver Sacks (The Man Who Turned Life Into Magic), who recently revealed in the New York Times that he has terminal cancer. I have had the pleasure of reading a number of Sacks’ books and seeing him give a terrific talk in Philadelphia a few years ago. Oliver Sacks is among the strongest of my inspirations for studying the brain!!

Oliver Sacks is a rare soul-reader among us, a golden heart that beats in resonance with an enlightened intellect and a refinement of feeling that finds the humanity cloistered in the deepest recesses of a damaged life. The stories he tells are the stories of his patients, but also his own; he knows and tells us, beautifully, how each experience touches and transforms his own, how each tale he narrates becomes part of his own narrative, his own life story. In this, and in writings such as Uncle Tungsten or Altered States, his New Yorker essay on hallucinatory drugs, we learn that to Oliver life is a grand experiment of the human condition, an experiment that can only bear fruit if we have the courage to engage fully with it. Oliver is the bravest man I know.

New antibiotic to fight resistant bacteria #Superdrug

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Researchers have discovered a new antibiotic unlike any other.  Published in Nature (currently free to access), this new antibiotic, found in the dirt, can potentially fight drug resistant bacteria! The New York Times provides a nice summary of the new finding:

The method, which extracts drugs from bacteria that live in dirt, has yielded a powerful new antibiotic. The new drug, teixobactin, was tested in mice and easily cured severe infections, with no side effects.

Better still, the researchers said, the drug works in a way that makes it very unlikely that bacteria will become resistant to it. And the method developed to produce the drug has the potential to unlock a trove of natural compounds to fight infections and cancer — molecules that were previously beyond scientists’ reach because the microbes that produce them could not be grown in the laboratory.

Teixobactin has not yet been tested in humans, so its safety and effectiveness are not known. Studies in people will not begin for about two years, according to Kim Lewis, the senior author of the article and director of the Antimicrobial Discovery Center at Northeastern University in Boston. Those studies will take several years, so even if the drug passes all the required tests, it still will not be available for five or six years, he said during a telephone news conference on Tuesday. If it is approved, he said, it will probably have to be injected, not taken by mouth.

Teixobactin is the most promising candidate isolated from 10,000 strains of bacteria that the researchers screened. In test tubes, it killed various types of staph and strep, as well as anthrax and tuberculosis. Tested in mice, it cleared strep infections and staph, including a strain that was drug-resistant. It works against bacteria in a group known as “Gram-positive,” but not against microbes that are “Gram-negative,” which include some that are major causes of drug resistant pneumoniagonorrhea and infections of the bladder and bloodstream. Dr. Lewis said researchers were trying to modify the drug to make it work against Gram-negative infections.

Teixobactin attacks bacteria by blocking fatty molecules needed to build cell walls, which is different from the way most antibiotics work. Those molecules are unlikely to change and make the microbes resistant, the researchers said. But if resistance does occur, Dr. Lewis predicted, it will take a long time to develop.

 

 

Worried about the #Ebola patient in New York City? – You must read this NYT article by Carl Zimmer! #science

zimmerA new case of ebola has been reported in New York City in a doctor who recently worked in West Africa. In a perfectly timed New York Times article, Carl Zimmer examines how contagious ebola is, and how easily it spreads. Turns out… compared to influenza, its not too bad. For all the New Yorkers out there, it is unlikely that anything less than direct contact with the patient, will put you at risk for infection with ebola (primary source here). As witnessed in Dallas, where even family members living in close quarters with Thomas Eric Duncan early in the disease course were not infected.

All the evidence scientists have gathered about Ebola, on the other hand, indicates that it spreads through contact with fluids from infected people. During an infection, the virus makes huge numbers of copies that contaminate the victim’s vomit, blood, diarrhea, urine and saliva.

Unlike the flu, Ebola does not lead to the kinds of coughs and sneezes that create a cloud of aerosols around a patient. Scientists who track the spread of Ebola have found that close contact with an infected person is necessary to become infected.

As mentioned in the CauseScience post earlier today about ebola ‘…the United States still only has 3 cases, emphasizing the ability of our healthcare system to effectively contain ebola.’

#Science Quotable: Paul Offit – Not getting the HPV vaccine makes NO SENSE

Why are adolescents and their parents embracing meningococcal and Tdap vaccines but not the HPV vaccine? One possible explanation is a clash between perception and reality, People just don’t understand how serious an infection HPV can be. In a typical year in the United States about 150 people die from meningococcus, four from tetanus, none from diphtheria, 20 from pertussis, and roughly 4,000 from cancers caused by HPV. People are more than 20 times more likely to die from HPV than from the other four diseases combined. – Paul Offit gives facts in his op-ed in NYT on HPV vaccination