Anti-science quotable: Scott Pruitt for the EPA

NO AMOUNT OF CAPS LOCK OR ANGRY FACE EMOJIS CAN EXPRESS MY DISCONTENT WITH THIS STATEMENT:

“I would not agree that [CO2] is a primary contributor to the global warming that we see,” Scott Pruitt said Thursday in an interview with CNBC’s Joe Kernen.

“I believe that measuring with precision human activity on the climate is something very challenging to do, and there’s tremendous disagreement about the degree of impact,” Pruitt said.

-It is challenging to measure the effect of human activity on climate

-But it’s been done it cuz #science

-and OVER 97% OF SCIENTISTS AGREE THAT THERE IS A LARGE IMPACT OF CO2 AND HUMAN ACTIVITY ON THE CLIMATE

TO THOSE IN POSITIONS OF POWER: PLEASE STOP DENYING THE HUMAN INFLUENCE ON CLIMATE CHANGE, AND PLEASE STOP PRETENDING THAT THERE IS DISAGREEMENT ABOUT THE SCIENCE.

Here’s more “analysis” on Pruitt’s comments. (I put “analysis” in quotes because I think most journalists are tired of having to cover climate deniers since they constantly have to go back to the OVERWHELMING evidence supporting climate change).

Here are some previous blog posts on climate change.

Having a climate change denier in charge of the EPA is like having a life-long vegetarian in charge of cooking steak. Or having a christian scientist run a cancer hospital. Or having an anti-public education supporter in charge of our public education. Have better analogies? Let us know.

@NIH observes #PRIDE month – How research impacts LGBTQ communities

NIH is observing PRIDE month this June with events on the NIH campus and the ‘telling our stories’ campaign. The Office of Equity, Diversity, and Inclusion (EDI), along with the Sexual & Gender Minority Research Office, and the National Institute of Minority Health and Health Disparities are bringing awareness this PRIDE month to how research impacts sexual and gender minority communities. See the NIH Director Francis Collins’ statement to NIH staff for pride month below.

Check out the NIH EDI website here for ‘Telling Our Stories’ and more. Or on twitter @NIH_EDI.

Dear Staff,

The National Institutes of Health (NIH) is committed to the principles of equal employment opportunity, diversity, and inclusion in our research and workplace.  As part of that commitment, the NIH will be celebrating this year’s Pride Month with a variety of activities that highlight the meaning of including the sexual and gender minority (SGM) community in our work.  The Office of Equity, Diversity, and Inclusion (EDI), the Sexual & Gender Minority Research Office, and the National Institute of Minority Health and Health Disparities are sponsoring several events that will address key areas of interest in working with SGM populations.  The goal of these activities is to understand, in very specific ways, how research impacts sexual and gender minority communities, and how best to conduct research with and for SGM populations.

The theme for this year’s NIH Pride Month is “Telling Our Stories, Claiming Our Power, Standing in Our Truth.”  This theme reflects our understanding of the importance of storytelling in the biomedical research setting.  In each of the four Pride Month events, we have the opportunity, perhaps for the first time, to look at research from a new and different perspective.

Throughout the month-long celebration, EDI will make available on their website video testimonials and written accounts of members of the NIH SGM community and their allies. Through this campaign, we will have the honor of hearing their stories and learning from their experiences.

Each of us has the ability and the responsibility to learn about, understand, and work for the interests of those groups that invite us and trust us to explore research opportunities within their communities.  I hope that during the month of Pride you will pause to reflect upon the diversity of the SGM population and the importance of including this community in our research and other related activities.  SGM research sits at the intersection of our ongoing commitment to equal employment opportunity, diversity and inclusion, and our mission of turning discovery into health.

For more information on the Pride events happening on the NIH campus, please visit http://edi.nih.gov/pride and follow EDI on twitter and Instagram at @NIH_EDI.

Sincerely yours,

Francis S. Collins, M.D., Ph.D.

Director

White House launches #Microbiome initiative!

WASHINGTON, DC – Today, the White House Office of Science and Technology Policy (OSTP), in collaboration with Federal agencies and private-sector stakeholders, is announcing a new National Microbiome Initiative (NMI) to foster the integrated study of microbiomes across different ecosystems, and is hosting an event to bring together stakeholders vital to advancing the NMI.

Microbiomes are the communities of microorganisms that live on or in people, plants, soil, oceans, and the atmosphere. Microbiomes maintain healthy function of these diverse ecosystems, influencing human health, climate change, food security, and other factors. Dysfunctional microbiomes are associated with issues including human chronic diseases such as obesity, diabetes, and asthma; local ecological disruptions such as the hypoxic zone in the Gulf of Mexico; and reductions in agricultural productivity. Numerous industrial processes such as biofuel production and food processing depend on healthy microbial communities. Although new technologies have enabled exciting discoveries about the importance of microbiomes, scientists still lack the knowledge and tools to manage microbiomes in a manner that prevents dysfunction or restores healthy function.

The NMI aims to advance understanding of microbiome behavior and enable protection and restoration of healthy microbiome function. In a year-long fact-finding process, scientists from Federal agencies, academia, and the private sector converged on three recommended areas of focus for microbiome science, which are now the goals of the NMI:

  1. Supporting interdisciplinary research to answer fundamental questions about microbiomes in diverse ecosystems.
  2. Developing platform technologies that will generate insights and help share knowledge of microbiomes in diverse ecosystems and enhance access to microbiome data.
  3. Expanding the microbiome workforce through citizen science, public engagement, and educational opportunities.

The NMI builds on strong and ongoing Federal investments in microbiome research, and will launch with a combined Federal agency investment of more than $121 million in Fiscal Year (FY) 2016 and 2017 funding for cross-ecosystem microbiome studies. This includes:

  • The Department of Energy proposes $10 million in new funding in FY 2017 to support collaborative, interdisciplinary research on the microbiome.
  • The National Aeronautics and Space Administration (NASA)proposes $12.5 million in new funding over multiple years to expand microbiome research across Earth’s ecosystems and in space.
  • The National Institutes of Health will invest an extra $20 million into microbiome research in grants in FY 2016 and FY 2017 with a particular emphasis on multi-ecosystem comparison studies and investigation into design of new tools to explore and understand microbiomes.
  • The National Science Foundation proposes $16 million in FY 2017 for microbiome research that spans the spectrum of ecosystems, species, and biological scales.
  • The U.S. Department of Agriculture proposes more than $15.9 million for FY 2017 to expand computational capacities for microbiome research and human microbiome research through the Agricultural Research Service, and approximately $8 million for FY 2017 to support investigations through the National Institute of Food and Agriculture of the microbiomes of plants, livestock animals, fish, soil, air, and water as they influence food-production systems.

In addition, following OSTP’s national call to action issued in January, more than 100 external institutions are today announcing new efforts to support microbiome science. These include:

  • The Bill and Melinda Gates Foundation will invest $100 million over 4 years to investigate and develop tools to study human and agricultural microbiomes.
  • JDRF will invest $10 million over 5 years to address microbiome research related to type 1 diabetes.
  • The University of California, San Diego, is investing $12 million in The Center for Microbiome Innovation to enable technology developers to connect with end users.
  • One Codex is launching a public portal for microbiome data, allowing greater access to this data for researchers, clinicians, and other health professionals.
  • The BioCollective, LLC, along with the Health Ministries Network, are investing $250,000 towards building a microbiome data and sample bank, and the engagement of underrepresented groups in microbiome research.
  • The University of Michigan, with support from the Howard Hughes Medical Institute and Procter and Gamble, will invest $3.5 million in the Michigan Microbiome Project to provide new research experiences for undergraduate students.

Click here to learn more about Federal involvement in microbiome research, and about all of the commitments and announcements being made today.

Anti-#Science Quotable: Senator James Inhofe on bees

scichecksquare_4-e1430162915812Senator James Inhofe has made some scientifically errant comments about bees and pesticides recently and so this week he was SCICHECKED!! Check the full page for lots of information about the science of bees and pesticides that is backed by actual studies!!

Sen. James Inhofe made misleading claims in a letter to the Environmental Protection Agency about the relationship between neonicotinoid pesticides and bees:

  • Inhofe said many scientists have concluded “that neonicotinoid pesticides only harm bees at dosages that are unrealistically high.” Actually, studies have shown that field-realistic doses of neonics can harm individual bees by inhibiting their immune system and navigation skills, among other effects.

  • Inhofe said there is consensus “that multiple factors are related to honey bee losses.” That’s true, but Inhofe ignored that researchers stress interactions among factors, e.g. neonics can lower a bee’s immune system, making it more susceptible to viruses, which can then cause death.

This is not the first time Senator James Inhofe has been way off the mark about something scientific. In fact, he seems to be a repeat offender when it comes to being anti-science or pro-psuedoscience.

@LamarSmithTX21 wrong on climate change… AGAIN. #tired @HouseScience @factcheckdotorg

scichecksquare_4-e1430162915812Representative Lamar Smith heads the House Committee on Science, Space, and Technology –  and is essentially as anti-science as you can get when it comes to climate change (see our many posts about Smith here). This week FactCheck.org gives Lamar Smith the SCICHECK – and no one should be surprised by the results.

Rep. Lamar Smith at a recent hearing claimed a new study published in the journal Nature Climate Change “confirms the halt in global warming.” It doesn’t. In fact, the authors of the paper write, “We do not believe that warming has ceased.”

At the March 16 House hearing, Smith also continued to criticize the Science paper. He said the paper was “prematurely published,” but the editor-in-chief of Science told us Smith’s claim is “baseless and without merit.” Smith also said that the NOAA researchers used “controversial methods” in their study, but the authors of the Nature paper cited by Smith said this wasn’t the case. In fact, they cite the Science paper as having “high scientific value.”

Overall, each study asked different scientific questions, the answers to which can both remain valid and correct, according to the Nature authors themselves.

The SCICHECK also goes on to remind us of the many other times Lamar Smith was way off base when it came to climate science… a trend even an untrained scientist like Smith should be able to recognize.

This is not the first time Smith, a Republican from Texas, has made false statements about climate science and the so-called “Karl study,” named after Thomas R. Karl, director of NOAA’s National Centers for Environmental Information and the Science paper’s lead author.

As we’ve written before, Smith claimed in October 2015 that “climate data has clearly showed no warming for the past two decades” and that NOAA scientists “altered the data” to get the results they presented in the Science study.

Check the whole article for the latest SCICHECK of Lamar Smith!!!

Measles and Pertussis outbreaks tied to vaccine refusal @NIHDirector #science

Parents have a responsibility not only to their own children, but to their communities—it’s only by achieving a very high level of population immunity that outbreaks can be prevented. Vaccination is particularly crucial for children with cancer and other diseases that cause immunosuppression. They cannot be vaccinated safely, but are at high risk of severe consequences if they are infected—and, thus, they depend on the community’s so-called “herd immunity” for protection against a potentially fatal illness.

While some parents continue to express concern about a possible link between vaccines and autism spectrum disorders, the original report claiming this connection has been debunked and retracted.  A large number of carefully designed follow up studies have been carried out, and the overwhelming weight of scientific evidence shows no evidence for such a link. That’s why it continues to be so important to get the word out to parents: Have your kids vaccinated.

Top 6 #GMO news stories from @GeneticLiteracy #GLPTop6!

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  1. Moms Across America claims GM salmon not kosher, but Jewish law, tradition say otherwise by Stephan Neidenbach

  2. Cellular clock may help improve cancer treatment, forensic science by Nicholas Staropoli

  3. Genetic engineering in Africa: Part 1: Bananas and Cassavas  || Part 2: Cautious embrace of biotechnology by Steven Cerier

  4. Enviro activists reject synbio solution for Indonesian palm oil-orangutan crisis by Nicholas Staropoli

  5. Life without allergies? Detecting genetically-based food allergies at birth by Meredith Knight

  6. Knowledge of genetic risks from personal DNA tests may not help in changing behavior by Arvind Suresh

House Science Committee and Chair Lamar Smith should focus on science, not politics #climate @NOAA

lamarChairman of House Committee on Science, Space, and Technology Lamar Smith thinks that the National Oceanic and Atmospheric Administration (NOAA) should focus on studying weather patterns rather than climate. Lamar Smith stated this, and a lot of misinformation, at a budget hearing for NOAA this week. Clearly Lamar Smith has failed Earth Science 101. While climate and weather are not the same thing, climate change can heavily influence weather patterns, and has been linked more and more strongly to EXTREME weather events.

“Instead of hyping a climate change agenda, NOAA should focus its efforts on producing sound science and improving methods of data collection,” said Smith. “NOAA should prioritize areas of research that significantly impact Americans today, such as ways to improve weather forecasting. Unfortunately, climate alarmism often takes priority at NOAA.”

Kathryn Sullivan, head of NOAA responded to Smith:

“NOAA forecasts help communities prepare and respond to weather events, including the severe storms that swept through Texas last year, tornado events across the mid-west and Florida, and the recent winter storm that struck the Northeast,” writes Dr. Sullivan in her statement. “But the greater demand for our services goes beyond just extreme weather.”

But perhaps the best response came from Rep. Eddie Bernice Johnson:

“It is clear to me that this investigation is unfounded, and it is being driven by ideology and other agendas,” says Johnson. “The majority has asserted, without offering any credible evidence, that NOAA and the climate science community at large are part of some grand conspiracy to falsify data in support of the significant role humans play in climate change. However, the overwhelming body of scientific evidence across many different fields has shown that this is not the case.”

In our opinion, Lamar Smith and the House Science Committee are an embarrassment to the American people, and the amazing science that is done here. It is very sad that NOAA and NOAA scientists are constantly being harassed by this political entity. (Check out @HouseAntiScienc on twitter)

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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!

When it comes to labs, is bigger always better? #science @NatureNews

Chris Woolston has written a nice feature in Nature this week titled, ‘Group dynamics: a lab of their own.’ The article describes many things a PI can consider when picking people for a lab, and how many people to pick. In his words:

Scientists around the world are working to solve the same basic formula: what number and mix of group members makes for the most efficient and productive lab?

As a member of a relatively large lab, where adding people to the group can come with many complaints from current members, I was intrigued by the actual data on productivity associated with adding members…

Bigger is better

Two studies published last year suggest that most labs could produce more papers and make a bigger splash by — perhaps unsurprisingly — bringing more people on board. One of these, a 2015 study of nearly 400 life-sciences PIs in the United Kingdom, found that the productivity of a lab — measured by the number of publications — increased steadily, albeit modestly, with lab size (I. Cook, S. Grange, & A. Eyre-WalkerPeerJhttp://doi.org/bcwf; 2015). In terms of sheer paper production, “it’s best for a lab to be as big as possible”, says co-author Adam Eyre-Walker, a geneticist at the University of Sussex, UK. Notably, the study found no sign that individual members become less productive or less efficient as labs grow. “Adding a team member to a large lab gives you the same return as adding one to a small lab,” Eyre-Walker says.

The second paper, a study of 119 biology laboratories from 1966 to 2000 at the Massachusetts Institute of Technology in Cambridge, found that productivity inched forward when an average-sized lab of ten members added people (A. Conti & C. C. Liu Res. Pol. 44, 16331644; 2015). But this study did detect limits: once lab size reached 25 people — an unusually high number achieved by very few labs — the addition of team members no longer conferred benefit. Further, a lab’s productivity tops out with 13 postdocs, the study found.

It looks as though my PI has created almost the perfect lab size. We are a bit over 25 with rotation students and technicians, but usually hover right around 13 postdocs… creepy. It turns out that their is some method, or at least data backing up, my PI’s madness.