Interesting news on the ancestry of Orangutans

An interesting bit of science news from my local University, the University of Copenhagen.

Extinct giant ape directly linked to the living orangutan

Researchers from the University of Copenhagen have succeeded in reconstructing the evolutionary relationship between a two million year old giant primate and the living orangutan. It is the first time genetic material this old has been retrieved from a fossil in a subtropical area. This allows the researchers to accurately reconstruct animal, including human, evolutionary processes way beyond the limits known today.

As the opening paragraph makes clear, this is an interesting piece of news, not only because of the results, but also because of the advancements in techniques this research has led to.

The news release from the university mostly focuses on how the expansion of the techniques are going to make broader research possible – for the actual results of the study, you’ll have to go to the article in Nature (behind a paywall)

European scientific or health personnel, please sign this manifesto

The Association to Protect the Sick of Pseudoscientific Therapies from Spain, and several other European organizations have gotten together to write a European manifesto against pseudo-therapies

It says, in part:

European directive 2001/83/CE has made –and still makes— possible the daily deceiving of thousands of hundreds of European citizens [10]. Influential lobbies have been given the opportunity to redefine what a medicine is, and now they are selling sugar to sick people and making them believe it can cure them or improve their health. This has caused deaths and will continue to do so until Europe admits an undeniable truth: scientific knowledge cannot yield under economic interests, especially when it means deceiving patients and violating their rights.

Europe is facing very serious problems regarding public health. Over-medicalization, multiresistant bacteria or the financial issues of the public systems are already grave enough, and there is no need to add to that gurus, fake doctors or even qualified doctors who claim they can cure any disease by manipulating chakras, making people eat sugar or employing “quantic frequencies”. Europe must not only stop the promotion of homeopathy but also actively fight to eradicate public health scams, which implicate more than 150 pseudo-therapies in our territory. Thousands of citizens lives depend on that. In fact, according to recent research, 25.9 % of Europeans have used pseudo-therapies last year. In other words, 192 million patients have been deceived [11].

Europe being concerned about the misinformation phenomena but at the same time protecting one the most dangerous types of it, health misinformation, is just not coherent. This is why the people signing this manifesto urge the governments of European countries to end a problem in which the name of science is being used falsely and has already costed the life of too many.

I do not fulfill the criteria for signing the manifesto, but I fully endorse it, and hope that any readers out there, who fulfill the criteria, will read the manifesto in full, and sign it.

It is about time that we got rid of pseudo-science in our health care in Europe.

Lazy linking

A few links to articles and blogposts that I think worth sharing

Laurie Penny has written a long-read article about not debating people: No, I Will Not Debate You

Civility will never defeat fascism, no matter what The Economist thinks.

Professor Julie Libarkin of Michigan State University has compiled a list of know harassers in academia

Rates of sexual abuse and harassment in academic science are second only to the military. It’s estimated that at least half of women faculty and staff face harassment and abuse and that 20 to 50 percent of women students in science, engineering, and medicine are abused by faculty. Those numbers are generally based on surveys, which are an important way of getting a handle on the problem and how it changes women’s career trajectories.

But when it comes to holding institutions accountable and making meaningful changes, naming perpetrators may be even more powerful.

Julie Libarkin has taken on the challenge of creating a database of harassers. She’s a professor at Michigan State University and she heads the Geocognition Research Laboratory. She’s compiled a list of some 700 cases of sexual misconduct in academia.

The human league: what separates us from other animals? by Adam Rutherford

You are an animal, but a very special one. Mostly bald, you’re an ape, descended from apes; your features and actions are carved or winnowed by natural selection. But what a special simian you are. Shakespeare crystallised this thought a good 250 years before Charles Darwin positioned us as a creature at the end of the slightest of twigs on a single, bewildering family tree that encompasses 4bn years, a lot of twists and turns, and 1 billion species.

Republicans hoped voters would forget they tried to kill Obamacare. They bet wrong. by Andy Slavitt

Andy Slavitt described his article thus on twitter:

Do you notice this phenomenon where your MOC behaves differently in odd numbered years and even numbered years? My @USATODAY column this week explains.

There’s overwhelming evidence that the criminal-justice system is racist. Here’s the proof. by Radley Balko

This is very relevant to my earlier post about the need for a reform in the US judicial system.

Has the Riemann hypothesis been proven?

Well, I guess we’ll find out on Monday.

One of the most important unsolved problems in mathematics may have been solved, retired mathematician Michael Atiyah is set to claim on Monday. In a talk at the Heidelberg Laureate Forum in Germany, Atiyah will present what he refers to as a “simple proof” of the Riemann hypothesis, a problem which has eluded mathematicians for almost 160 years.

Actually, it is highly unlikely that we will know on Monday, unless there is some obvious glaring error. Other people have to look at the proof, and it will take a while – when Grigori Perelman confirmed the Poincaré conjecture in 2003, it took until 2006 for it to be verified.

The Riemann hypothesis is one of the Millennium Prize Problems

Hayabusa-2’s probes successfully deployed

Given the current news cycle, this has probably escaped the attention of a lot of people, but there is some exciting science news.

The Hayabusa 2 mission by the Japan Aerospace Exploration Agency (JAXA) has been successful in landing two probes on the asteroid 162173 Ryugu. This is exciting news, since they will allow exploring the astroid’s surface.

Read more here:
Engadget: Japan’s Hayabusa 2 mission lands on target asteroid
The Japan Times: JAXA confirms tiny robots from Hayabusa2 landed on asteroid
BBC: Hayabusa-2: Japan’s rovers send pictures from asteroid

We are not as unique as we think we are

From ScienceDaily: Norway rats trade different commodities

Researchers of the University of Bern have shown for the first time in an experiment that also non-human animals exchange different kind of favours. Humans commonly trade different commodities, which is considered a core competence of our species. However, this capacity is not exclusively human as Norway rats exchange different commodities, too. They strictly follow the principle “tit for tat” — even when paying with different currencies, such as grooming or food provisioning.

In an experimental study, Manon Schweinfurth and Michael Taborsky from the Institute of Ecology and Evolution of the University of Bern tested whether common Norway rats engage in reciprocal trading of two different forms of help, i.e. allogrooming and food provisioning. Their test rats experienced a partner either cooperating or non-cooperating in one of the two commodities. To induce allogrooming, the researchers applied saltwater on the test rats’ neck, which is hardly accessible to self-grooming, so help by a partner is needed.

To induce food provisioning, partner rats could pull food items towards the test rats. Afterwards, test rats had the opportunity to reciprocate favours by the alternative service, i.e. allogrooming the partner after receiving food from it, or donating food after having been allogroomed. The test rats groomed more often cooperating than non-cooperating food providers, and they donated food more often to partners that had heavily groomed them before. Apparently, they traded these two services among another according to the decision rules of direct reciprocity.

“This result indicates that reciprocal trading among non-human animals may be much more widespread than currently assumed. It is not limited to large-brained species with advanced cognitive abilities,” says Manon Schweinfurth.

As is usually the case with ScienceDaily, the text is based upon the University’s press release, and it takes a bit of digging to find the actual paper, which is in Current Biology.

Reciprocal Trading of Different Commodities in Norway Rats

The prevalence of reciprocal cooperation in non-human animals is hotly debated [1, 2]. Part of this dispute rests on the assumption that reciprocity means paying like with like [3]. However, exchanges between social partners may involve different commodities and services. Hitherto, there is no experimental evidence that animals other than primates exchange different commodities among conspecifics based on the decision rules of direct reciprocity. Here, we show that Norway rats (Rattus norvegicus) apply direct reciprocity rules when exchanging two different social services: food provisioning and allogrooming. Focal rats were made to experience partners either cooperating or non-cooperating in one of the two commodities. Afterward, they had the opportunity to reciprocate favors by the alternative service. Test rats traded allogrooming against food provisioning, and vice versa, thereby acting by the rules of direct reciprocity. This might indicate that reciprocal altruism among non-human animals is much more widespread than currently assumed.

As the summary of the paper shows, the press release was overselling the unique human aspect of reciprocity using different commodities. This behavior have been observed in other primates. This study, however, is the first to show the behavior outside primates.

I always find it interesting when a study shows that a trait that is presumed to be unique for humans, or primates, actually exist among other animals. It makes you wonder if the reason why the traits are considered unique among humans/primates, is because we simply haven’t looked for them before.

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.