John Oliver discusses Scientific Studies

If you didn’t catch the latest episode of Last Week Tonight with John Oliver, be sure to do so. Summary here:

On Sunday’s Last Week Tonight, John Oliver debunked scientific studies that make outrageous claims. Oliver pointed to an example of an all too familiar subject of studies: Coffee. “In just the last few months, we’ve seen studies about coffee that claim it may reverse the effects of liver damage, help prevent colon cancer, decrease the risk of endometrial cancer, and increase the risk of miscarriage. Coffee today is like god in the old testament: It will either save you or kill you, depending on how much you believe in its magic powers.”

These studies can have serious consequences. Oliver explained that they are rarely replicated or fact checked, but that hasn’t stopped news organizations from actively reporting on the studies as truth. The contradictory nature of the these salacious studies can lead people to dismissing actual science that has been peer reviewed… like climate change.

There are always scientific experiments that haven’t yet been replicated or that are just waiting to be disproven. That is because science is a work in progress… we are always improving techniques, and learning more about subjects. I think the real problem lies with the media taking scientific evidence and portraying it as “fact” in order to boost viewership of the story. While scientists can always work harder to improve communication skills, this is a two-way street, and the media simply needs to do a better job of reporting on science.

All you need to know about #ASAPbio and preprints

Excellent piece in F1000 by Gary McDowell about preprints, the purpose of the ASAPbio meeting, potential issues and benefits, and what we can expect as a result. For anyone who has questions on this issue, this is for you!

Junior biomedical scientists and preprints

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!

#ASAPbio is currently discussing the future of #science publication! #scicomm #starstuddedcast

Just in case you weren’t aware, ASAPbio is currently underway and is likely going to influence the future of science publication!!

Accelerating Science and Publication in Biology (ASAPbio) will be an interactive meeting to discuss the use of preprints in biology held on February 16-17, 2016. The meeting will be streamed online, and we welcome participation from all interested parties through this website and on Twitter (#ASAPbio).

For background on the issues facing science publication, especially in biomedical science and biology, check out this primer from Nature last week (Does it take too long to publish research?). We here at CauseScience think that the answer to that title is a resounding YES!! One option that ASAPbio is considering are preprints – commonly used in other science fields. Nature this week featured another article related to ASAPbio about preprints (Biologists urged to hug a preprint).

For up to date info on the conference, check out the twitter hashtag #ASAPbio, which thus far has included tweets from well-known scientists, and fun pictures of former NIH directors and Nobel Laureates!! Or just visit the ASAPbio website!!

Definitely exciting to see people discussing the problems of science publication, but more importantly, discussing potential solutions!!

The 12 days of #OpenScience thanks to PLoS ONE!

PLoS blogs is featuring the “12 days of Open Science“. Enjoy this creative take on the 12 days of Christmas with insights from articles featured in PLoS ONE!

It’s starting to get colder in San Francisco, and the year-end holidays are soon to be upon us. This has made all of us on the PLOS ONE team excited to spend some time with our loved ones and general merriment. So for a little festive fun, here are 12 PLOS ONE articles that scientifically remind us of the verses in the classic holiday tune “12 Days of Christmas.”

1. Partridge in a Pear Tree

partridge 2

It’s not all pear trees for these partridges. In “Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection,” the authors explored the possible role of red-legged partridge immunity when wild populations restocked with partridges raised in captivity are exposed to disease and stress.

2. Turtle Doves

Turtle Doves

If you’ve ever wondered where the European turtle dove migrates throughout the year, the authors of “Migration Routes and Staging Areas of Trans-Saharan Turtle Doves Appraised from Light-Level Geolocators” studied wild turtle doves’ routes and winter resting spots for a year using lightweight GPS.

3. French Hens

french hens

There is the possibility that we may pick up our parents’ idiosyncrasies, but the authors of “Parents and Early Life Environment Affect Behavioral Development of Laying Hen Chickens,” wanted to see if the same could be true for chickens. The researchers studied whether parents and environment could affect anxiety and severe feather pecking in their young.

4. Calling Birds

calling birds

Scientists observed how New Caledonian crows interacted in order to potentially as a team in “New Caledonian Crows Rapidly Solve a Collaborative Problem without Cooperative Cognition.” They found that wild-caught New Caledonian crows would pass a stone from one to the other and then drop the stone into a hole that collapsed a baited platform. This showed that they could instinctively solve complicated tasks together, but the researchers did not discover any evidence that their problem-solving skills were based on comprehension of cooperation.

5. Golden Rings

golden rings

Every two years, top athletes from around the world compete in the Olympic Games in search of the gold medal. In “The Road to Gold: Training and Peaking Characteristics in the Year Prior to a Gold Medal Endurance Performance,” scientists researched whether these athletes taper their workouts before their competitions and how this affects their performance. The researchers found that gold medalists did not taper their workouts prior to competitions, as is suggested as the best practice.

6. Geese a-Laying

geese a-laying

More and more wild Greylag geese may be a-laying their heads in more northern areas in a possible reaction to climate change, according to “Latitudinal-Related Variation in Wintering Population Trends of Greylag Geese (Anser Anser) along the Atlantic Flyway: A Response to Climate Change?

7. Swans a-Swimming

swans a-swimming

The authors of “Molecular Detection of Hematozoa Infections in Tundra Swans Relative to Migration Patterns and Ecological Conditions at Breeding Grounds,” looked into how blood parasites can spread between wild tundra swans and whether where they swim when migrating has any effect. The infection of blood parasites was considerably different in the populations of tundra swans in Alaska with the highest prevalence in swans whose breeding grounds were warmer and less windy, according to the researchers.

8. Maids a-Milking

maids a-milking

Can you detect biomarkers in cow’s milk with an ordinary smartphone? In “Calling Biomarkers in Milk Using a Protein Microarray on Your Smartphone” the authors explore the possibility of doing this with the potential application of on-site food safety, health monitoring, and environmental tests.

9. Ladies Dancing

ladies dancing

In “Psychophysiological Responses to Salsa Dance,” researchers studied whether dance provides enough exertion to promote fitness and overall health benefits in the same way that traditional forms of exercise can provide. From their experiments, the authors found that salsa dance likely does provide enough energy expenditure to deliver overall health and fitness benefits, but also that people find it fun, which may mean that people will continue to practice dance.

10. Lords a-Leaping

lords a-leaping

Our bodies anticipate the impact back onto the ground after we jump, but the authors of “Motor Control of Landing from a Jump in Simulated Hypergravity” wanted to see how bodies would react when gravity was increased. Through their experiments, the authors found that while the preparation for jumping is modified in hypergravity, the remainder of the jump remains the same.

11. Pipers Piping

pipers piping

Researchers studied ant nest beetle piping to see whether the sounds they may help them in their predation of ants in “The Pied Piper: A Parasitic Beetle’s Melodies Modulate Ant Behaviours.” The experiments performed by the authors suggest that the beetles mimic the queen ant and use this skill to trick the workers into being treated like the queen. Visit SoundCloud to listen to these parasitic beetles’ melodies.

12. Drummers Drumming

drummers drumming

Tapping to the beat of your own drum, may be an un-related rhythmic skill than remembering rhythms, according to the authors of Evidence for Multiple Rhythmic Skills. The researchers explored how rhythmic skills relate to each other and what implications that could have for processing language.

Take the ASAPbio survey! #ASAPbio #publications

Accelerating Science and Publication in Biology (ASAPbio) will be an interactive meeting to discuss the use of preprints in biology held on February 16-17, 2016. The meeting will be streamed online, and all interested parties can participate through the website and on Twitter (#ASAPbio).

Most scientists believe that the present publication system is in need of change. Of many possible innovations in communicating biological research, the widespread use of preprints has the potential to be both transformative and feasible in the near-term. The purpose of this meeting is to gather scientists and a variety of other stakeholders for focused discussions on preprints and the role that they might play in catalyzing scientific discovery, facilitating career advancement, and improving the culture of communication within the biology community. The meeting will identify actionable next steps that emerge around areas of consensus, and the organizing committee and other interested participants will be involved in subsequent follow-through.

For those of you interested in these matters, please take less than 5min to fill out this survey! Thanks!!

The ethics of authorship in scientific publication, explained @TheConversation

Tackling unethical authorship deals on scientific publications

By Isaac Santos; Carlos Duarte, University of Western Australia; Damien Maher; Peter Macreadie, University of Technology, Sydney, and Scott G Johnston

The research excellence of academics is often measured by the quantity and quality of their scholarly publications. But how do we know that all authors listed on a publication have actually been involved in the research?

Is our “publish or perish” culture encouraging the development of unethical, fraudulent co-authorship deals?

The number of authors on scientific papers has been growing. In 2011, the average number of authors on a paper stood at 4.5, up from 3.8 in 2007. Papers listing hundreds – even thousands – of authors are not uncommon.

Authorship has become a core currency of modern science, and the main means to assign credit to researchers. Assigning authorship responsibly and ethically is essential to the health of any research group and the broader scientific community.

Sharing credit for scientific discoveries is a challenge. The growing number of authors listed on papers demands that individual professional ethics be stronger than ever.

If willing to do so, experienced group leaders can easily take advantage of inexperienced scientists, and authorship credit will always flow up the rank ladder. The “Matthew Effect” in science describes how senior scientists can easily benefit through credit that belongs to junior co-authors.

This places junior scientists in difficult positions to argue against any unfair authorship deals. Group leaders may just quietly accept, or even enforce, unfair authorship deals to further build their credentials, and retain leadership status.

While data are scarce and hard to come by, the pressure to publish may create incentives for growing numbers of unethical authorship deals.

These deals come in many names including coercive, honorary, guest, gift, ghost, and duplicated authorship. Minimising unethical authorship deals is challenging when academics may be unacquainted with formal authorship criteria.

Take the test

Many academics may have experienced or heard about unethical authorship deals. If you have at least a few scientific papers under your belt, are you aware of any of the following situations?

  1. A senior academic is included in publications just because they are the gatekeeper to facilities funded with taxpayer money.
  2. A senior academic adds additional authors to a paper even if the first author (often a junior academic) never spoke to these additional authors or has no idea about their contributions.
  3. A junior academic adds a senior academic to a paper simply to improve career prospects, or potentially bring prestige to facilitate the publication of the paper.
  4. A senior academic expects to be given authorship on all papers produced by their group regardless of whether they contributed to the research or not.
  5. Large research groups including all members in all papers even when there has been negligible contribution from some of them.

If you are a junior academic who answered “no” to all the above questions, you have good reasons to be proud of your group’s ethics.

If you answered “yes” to any, it may be time to consider your career and leadership options. You may be part of an undeclared, unethical scheme in which junior academics do the work while the most senior academics take undue credit and reap the rewards.

All the options listed above breach our ethics and codes of conduct, and artificially inflate the record of senior academics.

Unethical conduct around authorship is akin to a lie and undermines the entire discipline of science.

Occasionally such behaviour is exposed. For example, a senior academic lending his name to a paper had to argue that he did not participate in the research so he could escape a more serious case of academic misconduct. Such cases have led some major journals to issue statements requesting details on the contributions of all co-authors.

Incentives in the university system

Our highly competitive “publish or perish” culture is well established and encouraged by reward processes in universities and funding agencies.

A scientist’s publication record is considered a major criteria influencing success in prestigious Australian Research Council (ARC) grants or promotion. In an environment of increasing competition, universities need to develop strategies to maximise funding outcomes.

A common Australian university strategy is to invest most of the resources into a few science stars that are expected to raise additional funding from the ARC.

This approach has at least one major flaw. The relationship between an academic’s productivity versus dollars invested is unlikely to grow linearly.

At a given point, the research outputs will reach the point of diminishing returns and continuing institutional investment is unlikely to further increase productivity. Personal productivity can only be squeezed so far. Researchers have a finite capacity to meaningfully contribute as authors.

At this point, unethical authorship schemes may come into play and quickly gather momentum.

Academics who control substantial university resources may suddenly become untrained managers of large research groups. They become science politicians. These new managers may still be listed as authors even though effective management requires re-allocation of time away from scientific endeavours.

The incentive for senior academics to become managers should be better pay, not contractual key performance indicators (KPI) that value their inclusion as an author on every paper produced by a work unit for which they are responsible.

The way forward

Challenging spurious authorship claims of senior academics is perceived as a career suicide for junior academics in an environment of short-term contracts controlled by the group leader.

The senior academic knows that if the junior collaborator objects, the choice of whistleblowing is daunting. The junior academic may think it is far easier and safer to just add another name to a multi-authored paper if this culture is already established.

In this case, the junior academic offers payment (by authorship) to the senior academic in return for protection in an uncertain academic environment.

Such authorship schemes erode both scientific and personal integrity. They essentially amount to publication prostitution. So how do we prevent them?

Senior academics should carry most of the burden and lead from the front by example. High standards of individual ethics are critical, as is creating and fostering a culture in which personal ethics are more valued than research outputs.

Educating junior academics not only on the importance of publishing, but also on how to properly attribute authorship is a good starting point.

The requirement of a significant intellectual input requiring contributions to designing and/or conducting the study as well as analysis and writing, must not be waived for anyone.

Follow the codes

There are national and international guidelines and codes of conduct that establish clear criteria for shared authorship. For simplicity, some of us follow an authorship index that works quite well in our broad field of natural sciences.

In a research environment with strong ethics, the leading author should offer authorship to all who may have a legitimate authorship claim. They should also be open to considering co-authors whose role may not have been evident, which can occur in large interdisciplinary efforts.

The invited academics should then use even stronger personal ethics to decide whether they should accept authorship or opt for a warm acknowledgement. In this way, excluding a colleague who has made a sufficient contribution is avoided. Unfair exclusions can also poison academic environments.

But in a research environment where professional ethics are weak, undeserving authors are unlikely to decline invitations to become authors. Here, the opposite approach should be adopted by the leading author. Co-authors are invited only when the leading author has confidence the colleague made a large enough contribution to warrant authorship.

When weak ethics or self-interest prevents action from senior academics, junior academics should find creative ways to stand up and retain credit for their discoveries without committing career suicide.

Confidential conversations with independent mentors – that may include an ethics officer or a director of research – can start a process of top down change without threatening the career of the junior academic.

The future

If junior academics don’t take action when facing unethical authorship deals, the worst may happen.

If junior academics accept the masked exploitation as they develop a publication portfolio, they replicate the unethical behaviour of their senior peers and jointly break codes of conduct.

If this unethical behaviour is passed from one generation to the next, the scale of the problem will only increase. With different generations of scientists vying for the same pool of funding, a publication arms-race is likely to develop, to the detriment of personal and academic integrity.

Ending a culture of unethical authorship deals can be quite challenging. Preventing these deals in the first place is a responsibility of the entire scientific community.

The Conversation

This article was originally published on The Conversation.
Read the original article.