Scooped science gets a second chance

One of the biggest fears of scientist doing research is getting scooped by other scientist, making their research unpublishable. Now, there is good news to scientists, or at least biologist. PLOS Biology has a new policy when it comes to scooped research.

Scientific research can be a cutthroat business, with undue pressure to publish quickly, first, and frequently. The resulting race to publish ahead of competitors is intense and to the detriment of the scientific endeavor. Just as summiting Everest second is still an incredible achievement, so too, we believe, is the scientific research resulting from a group who have (perhaps inadvertently) replicated the important findings of another group. To recognize this, we are formalizing a policy whereby manuscripts that confirm or extend a recently published study (“scooped” manuscripts, also referred to as complementary) are eligible for consideration at PLOS Biology.

Being scooped is loosely defined as when two independent groups studying the same system produce the same or similar results, and one group publishes their work first. Being scooped is often considered to devalue the second, complementary study; many journals will reject it citing lack of novelty. However, there is a self-evident benefit to publishing complementary research, and at PLOS Biology, we consider that two papers from two groups independently identifying the same phenomenon in parallel increase the confidence in the results of the work.

This new policy, acknowledging the value of complementary studies, therefore addresses the current concern regarding the reproducibility, or lack thereof, of scientific findings. Currently, the gold standard for demonstrating that an article is based on solid results is a replication study. These studies are generally conducted after publication and are considered critically important for supporting and advancing scientific theories. We argue that the “organic” replication of a complementary study is even better than a post-hoc and often costly replication study for supporting conclusions. There are other efforts underway to improve reproducibility and encourage replication, such as the Reproducibility Project: Cancer Biology (https://osf.io/e81xl/), as well as endeavors to implement high-quality reporting. With consideration of complementary research, PLOS Biology will support and promote scientific reproducibility and replication.

Of course there is a time limit on publishing complementary results

Under our newly codified policy, authors of a complementary study have six months from the publication or posting (to a preprint server) of the first article to submit their manuscript to PLOS Biology. We hope that authors will use these six months to fully support and potentially extend the results of the first article. Complementary research submitted beyond the six-month period may still be considered, depending on individual circumstances. All submissions must still meet our editorial requirements for depth of study and potential impact.

I think this is a great move by PLOS Biology and as they say, it should help address the widespread concern with reproducibility of scientific results.

The time limit for complementary results makes sense, but I hope that PLOS Biology is open for papers reproducing older results, if the papers are important enough.

Lazy linking

A few thing I have found of interest.

SF will wipe thousands of marijuana convictions off the books

San Francisco will retroactively apply California’s marijuana-legalization laws to past criminal cases, District Attorney George Gascón said Wednesday — expunging or reducing misdemeanor and felony convictions going back decades.

The unprecedented move will affect thousands of people whose marijuana convictions brand them with criminal histories that can hurt chances of finding jobs and obtaining some government benefits.

Proposition 64, which state voters passed in November 2016, legalized the recreational use of marijuana in California for those 21 and older and permitted the possession up to 1 ounce of cannabis. The legislation also allows those with past marijuana convictions that would have been lesser crimes — or no crime at all — under Prop. 64 to petition a court to recall or dismiss their cases.

This is an important move. A lot of people have been jailed in the past for crimes which is no longer on the books, and it is only fair that they get released.

Science behind bars: How a Turkish physicist wrote research papers in prison

Thousands of academics in Turkish universities stand accused of either having supported terrorism or the attempted coup against President Recep Tayyip Erdoğan in July 2016. Theoretical physicist Ali Kaya is one of them. He was arrested three months after the failed coup and held for more than a year before his trial took place. On 20 December, a court declared him guilty of being a member of a terrorist organization and sentenced him to six years of imprisonment — but released him early owing to the time he had already served in prison while awaiting trial. Kaya says that he is innocent and is appealing against the verdict. In the meantime, he has been suspended from his academic post, and he has yet to learn whether his university, Boğaziçi University in Istanbul, plans to fire him or to await the outcome of the appeal.

This story shows how Turkey has become a totalitarian regime, and how scientists can persevere under horrible circumstances.

Your Grandma Was a Chain Migrant!

Jennifer Mendelsohn, a freelance writer based in Baltimore, has a low tolerance for bad faith. Last summer, after Stephen Miller, the White House senior policy adviser, went on television to support a bill that would penalize immigrants who didn’t speak English, Mendelsohn took to Twitter. “Miller favors immigrants who speak English,” she began. “But the 1910 census shows his own great-grandmother couldn’t.” Her tweet, which included a photograph of a census document indicating that Miller’s ancestor spoke only Yiddish, went viral. “It’s hilarious how easy it is to find hypocrisy,” Mendelsohn said. “And I’m a scary-good sleuth.”

Ursula K. Le Guin, the spiritual mother of generations of writers; John Scalzi pays tribute

World’s oceans rise to hottest temperatures ever recorded ‘by far’

‘Long upward trend that extends back many decades does prove global warming’

Not that we really need any more evidence.

Spiritual hyperplane

How spiritualists of the 19th century forged a lasting association between higher dimensions and the occult world

Interesting bit of history.

Do video gamers have an advantage in learning?

Perhaps, at least according to ScienceDaily, who has a write up of a press release on a paper Games people play: How video games improve probabilistic learning. The paper is unfortunately behind a pay-wall, but the ScienceDaily write-up describes it thus:

Neuropsychologists of the Ruhr-Universität Bochum let video gamers compete against non-gamers in a learning competition. During the test, the video gamers performed significantly better and showed an increased brain activity in the brain areas that are relevant for learning. Prof Dr Boris Suchan, Sabrina Schenk and Robert Lech report their findings in the journal Behavioural Brain Research.

This sounds interesting, and would obviously be good ammunition for all the young people wanting to play more computer.

Unfortunately, from the rest of the description of the article, it might be too early to start celebrating.

The research team studied 17 volunteers who — according to their own statement — played action-based games on the computer or a console for more than 15 hours a week. The control group consisted of 17 volunteers who didn’t play video games on a regular basis. Both teams did the so-called weather prediction task, a well-established test to investigate the learning of probabilities. The researchers simultaneously recorded the brain activity of the participants via magnetic resonance imaging.

There are some serious problems with the paper, as it is described.

First of all, the sample is tiny – there is 34 people in it. And since it consists of volunteers, the participants are self-selected.

Also, it appears that there were no blinding. We know that there are many ways to affect how well someone does on a test – even by just reminding people of stereotypes just before the test. This might be the case here.

On top of that, they have used a type of test, which could very likely appeal to the same people, to whom computer games are appealing.

There might be something here, but let’s not start forcing kids to play computer games just yet.

Honoring Inge Lehmann

On May 15th, the University of Copenhagen will hold a symposium celebrating Inge Lehmann. As part of the celebration, a monument honoring her and her discovery will be unveiled on Frue Plads. Frue Plads is a square located just in front of the historical buildings of the University, and the square contains busts of prominent alumni of the university, including several prominent scientists (like Niels Bohr), but not, to my knowledge, any honoring a woman.

So, who is Inge Lehmann, and why is she honored by the University of Copenhagen?

To answer that, let’s go to wikipedia’s entry on her:

Inge Lehmann ForMemRS (13 May 1888 – 21 February 1993) was a Danish seismologist and geophysicist. In 1936, she discovered that the Earth has a solid inner core inside a molten outer core. Before that, seismologists believed Earth’s core to be a single molten sphere, being unable, however, to explain careful measurements of seismic waves from earthquakes, which were inconsistent with the Earth having a single molten core. Lehmann analysed the seismic wave measurements and concluded that Earth must have a solid inner core and a molten outer core to produce seismic waves that matched the measurements. Other seismologists tested and then accepted Lehmann’s explanation. Lehmann was also the longest-lived woman scientist, having lived for over 104 years.

The discovery of the solid inner core was done through the analysis of P-waves, and was published by her in her 1936 paper P’. What she observed was basically that P-waves didn’t get deflected by the (outer) core, as might be expected, but that it deflected on something else, further in, leading her to believe that there was an inner core inside the core. We now talk of the outer core (which is liquid) and the inner core (which is solid).

Her ideas were widely accepted within a few years, but it wasn’t until computers came around, that they could be demonstrated to be true through computer calculations. This happened in 1971.

Inge Lehmann is largely unknown in Denmark outside seismology and geophysics circles, but she is probably one of the most important scientists to ever come out of the country, which can be witnessed through the fact that the American Geophycical Union (AGU) has named a medal after her, awarded for “outstanding contributions to the understanding of the structure, composition, and dynamics of the Earth’s mantle and core.”

As a side note. When reading up on Lehmann, who I had heard about, but didn’t know too many details about, I noticed that she didn’t finish her study until she was 32, having taken a break for several years, working in an insurance company. I can’t help think about how the current policy of pushing people through their study would have led her to drop out, and thus she would never have had the chance to make her discovery.

The Neolithic transition in the Baltic region

Through ScienceDaily, I have just come across an interesting open access paper in Current Biology The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers

The paper takes a look at the driving force between Neolithic transition in the Baltic and parts of Ukraine, where the Neolithic transition happened later than in Western and Central Europe. The paper describes the Neolithic transitions and the context for the paper thus:

In Europe, the Neolithic transition marked the beginning of a period of innovations that saw communities shift from a mobile lifestyle, dependent on hunting and gathering for survival, to a more sedentary way of life based on food production. This new lifeway, which originated in the Near East ∼11,500 calibrated years before present (cal BP) [5, 6], had arrived in southeast Europe by ∼8,500 cal BP [7], from where it spread quickly across the continental interior of Europe and introduced animal husbandry, cultivated cereals, pottery, and ground stone tools to the region. There is a long-standing debate among archaeologists whether this spread was due to the dispersal of farmers into new lands (i.e., demic diffusion) or horizontal cultural transmission [8]. Genetic evidence suggests that these cultural and technological changes were accompanied by profound genomic transformation, consistent with the migration of people of most likely Anatolian origin [9, 10, 11, 12]. In contrast to central Europe, the adoption of agriculture in northern and eastern parts of this continent, in the areas which encompass modern-day Latvia and Ukraine, was slow and relatively recent [13, 14, 15, 16]. Although some features of the Neolithic package, such as ceramics, appeared as early as 8,500–7,500 cal BP [17, 18], agriculture was not adopted as a primary subsistence economy until the Late Neolithic/Bronze Age [13, 14, 15, 16, 19].

So, in other words, the Neolithic transition has generally be found to be caused by outsiders immigration into the region, taking the technology with them. The question was, whether that was also the case for those regions which changed later.

According to the paper, the analysis shows that there were little genomic transformation in the area studied, leading to the conclusion that the technology was transferred through trade rather than through immigration into the area.

It is quite interesting to see how the fairly new genetic analysis techniques are used to settle old discussions in different fields – here archaeology.

 

Problems in Chinese clinical trials

I came across this story some weeks ago, and have been wondering why it hasn’t received more widespread coverage in the science-sphere and in the news.

80% of data in Chinese clinical trials have been fabricated

A Chinese government investigation has revealed that more than 80 percent of the data used in clinical trials of new pharmaceutical drugs have been “fabricated“.

The report uncovered fraudulent behaviour at almost every level, and showed that some pharmaceutical companies had hidden or deleted records of potentially adverse side effects, and tampered with data that didn’t meet their desired outcomes.

In light of the findings, 80 percent of current drug applications, which were awaiting approval for mass production, have now been cancelled.

The investigation, led by the Chinese State Food and Drug Administration (SFDA), looked at data from 1,622 clinical trials for new pharmaceutical drugs currently awaiting approval. The applications in question were all for Western medicine, not traditional Chinese medicine.

The SFDA found that the more than 80 percent of the data failed to meet analysis requirements, were incomplete, or totally non-existent.

The lack of general coverage worried me, as this seems like a major story, so I decided to try to dig deeper into the story before writing about it.

This proved to be wise, as the first reports wasn’t as complete as one could have wished.

CFDA: reports of clinical trial data fraud ‘not fact based’

The Chinese Food and Drug Administration (CDFA) has fired back on lack of context in media reporting “80% of China’s clinical trial data are fraudulent.”

According to this article, most of the trials were voluntarily withdrawn during a self-examination process, and were thus not found to be fraudulent by the CFDA. Another article adds a bit more details:

Asia Regulatory Roundup: CFDA Investigates Trial Sites Over Data Integrity

China’s Food and Drug Administration (CFDA) has opened investigations into 11 clinical trial sites and contract research organizations (CROs) as part of a data verification drive initiated last year. The regulator suspects the sites and CROs generated fraudulent clinical trial data to support 27 new drug applications.

CFDA released details of the investigations as part of a breakdown of the numbers associated with the self-audit of drug applications by organizations seeking approval in China. Of the 1,622 applicants asked to carry out the self-examination in July 2015, 1,193 organizations withdrew their submissions voluntarily after receiving the regulator’s request. CFDA allowed applicants to withdraw their filings without facing punishment. As 193 of the applicants were exempt from clinical trials, the withdrawals amount to 83% of all the submissions that went through the self-audit.

The regulator is seeking to dispel reports all of the applications were withdrawn because their data were fraudulent. While CFDA acknowledges some of the applications included false data, deliberately or by mistake, others were withdrawn because of more prosaic failings. Some of the withdrawals were triggered by recognition of failures to comply with good clinical practices (GCPs). Others were a result of the clinical trial data falling short of what is needed to demonstrate the safety and efficacy of a medicine

So, it seems like it is overstating it to claim that over 80% of all Chinese clinical trials contained fraudulent data.

It does, however, seem like one could make the claim that there have been found widespread problems with the data in Chinese trials – either through self-examination or through official data verification – otherwise, why would so many results be voluntary withdrawn?

I am happy to see that the Chinese authorities are following up with investigations into clinical trial sites and contract research organizations.