Simmons and colleagues conduct computer simulations and two experiments that show how significant results can easily be achieved for a research hypothesis that is false. They show that flexibility --or as they call it: researcher degrees of freedom --in four areas make it more likely to find significant effects for a false hypothesis:

1. Flexibility in choosing the dependent variables reported: When researchers flexibly analyze two related dependent variables, this already almost doubles the probability of finding a positive result for a false hypothesis.

2. Flexibility in choosing the sample size: When researchers stop data collection, find no significant result, and collect additional data before checking for the same effect, this increases the probability of finding a positive result for a false hypothesis by 50%.

3. Flexibility in the use of additional variables included in the analyses: When researchers include additional variables in the analyses, false positive rates more than double.

1. Flexibility in the number of experimental conditions reported: When researchers collect data in three experimental conditions and flexibly decide whether to report the result of comparisons between any two conditions or all three, this more than doubles the false positive rate.

If researchers used research practices where they used all four flexibilities, they would, overall, be more likely to find positive results although the underlying hypothesis was indeed false.

Rosenthal addresses the 'file drawer problem', a questionable research practice where only studies that showed the desired result would be published and all other studies would land in the 'file drawer' and thus unknown to the scientific community.

In the extreme case, this could mean that, if a specific effect did not exist in reality, the 5% of studies that (due to statistical error allowed) find this effect get published and discussed as if the effect were true, whereas 95% of studies do not (and rightly so) find the effect, but are tucked away in a file drawer. This problem hinders scientific progress, as new studies would build on old, but false, effects.

Rosenthal introduces a way to assess the size of the file drawer problem, the tolerance to future null results: calculating the number of studies with null results that would have to be in a file drawer before the published studies on this effect would be called into question.

Nosek and colleagues argue that scientists are often torn between "getting it right" and "getting it published." While finding out the truth is the ultimate goal of research, more immediately, researchers need to publish their work to be successful in their profession.

A number of practices, such as the establishment of journals emphasizing reports of non-significant results, are argued to be ill suited for improving research practices. To reconcile the two seemingly-at-odds motives, Nosek and colleagues suggest measures such as lowering the bar for publications and emphasizing scientific rigor over novelty, as well as openness and transparency with regard to data and materials.

John, Loewenstein and Prelec conducted a survey with over 2,000 psychologists to identify to what extent they used questionable research practices (QPRs). The respondents were encouraged to report their behavior truthfully, as they could increase donations to a charity of their choice by giving more truthful answers.

Results showed that a high number of psychologists admitted to engaging in QRPs. Almost 70% of all respondents admitting to not reporting results for all dependent measures and around 50% of respondents admitting to reporting only studies that showed the desired results.

Moreover, results showed that researchers suspected their peers also occasionally engaged in such QRPs, but that psychologists thought that there was generally no good justification for engaging in QRPs.

Howard and colleagues examine how the file drawer problem---that is, the tendency of researchers to publish positive results but not negative or inconclusive results--affects a body of research literature. They compare "old," existing bodies of literature that could be suffering from the file drawer problem with a newly constructed body of literature guaranteed to be free of the file drawer problem, which they achieved by conducting new studies.

This investigation suggests that some bodies of literature are supported as relatively file-drawer-free, while other bodies of literature raise concern and kindle further studies on the effects they include.

Greenwald examines how research practices discriminate against accepting the null hypothesis (that an effect does not exist). Using a simulation, he suggests that too few publications accept the null hypothesis, and that a high proportion of publications falsely reject the null hypothesis when it would have held.

Greenwald further debunks traditional arguments about why a null hypothesis should not be accepted, and suggests ways to improve research practices to improve the acceptance of accepting the null hypothesis.

Fanelli assessed more than 2000 papers from different scientific disciplines and found that the proportion of studies reporting support for their hypotheses is higher in disciplines such as psychology or economics as compared to disciplines such as space science. It is concluded that both the type of hypotheses tested and the rigor applied in these tests differ between fields.

Button and colleagues study the average statistical power of studies in neuroscience, and conclude that it is low. They highlight that low power does not only mean that studies have a lower chance of detecting a true effect, but that when using such low-powered studies, it is also becomes less likely that a significant effect indeed reflects a true effect.

It is argued that using studies with low power may seem efficient at the first glance, because less money is spent on subjects. However, because future research could be building on an erroneous line of investigations, low-powered studies are inefficient in the long-run.

This study presents an efficient method to produce neural stem cells from human pluripotent stem cells.

The system presented in this study enables the creation of NSC banks, increasing cell therapy applications.

This study examines the effects on the developing fetus of congenital cytomegalovirus infection.

In this study, Grief et al. used electron microscopy to localize dengue virus in infected mosquito cells.

They concluded that the smooth membrane structures are an important site for the production of virus particles.

Tang’s article highlights the impact of ZIKV infection on both cell death and dysregulation of the cell cycle.

In this article, the authors were able to detect the Brazilian Zika virus in amniotic fluid and compare its genome to other Zika strains and flaviviruses. In doing so, they hoped to find out if there had been recombination events between them.

The authors collected amniotic fluid samples from women whose fetuses were diagnosed with microcephaly, extracted DNA purified virus particles, and analyzed the samples with qRT-PCR.

They found that the different viruses share 97–100% of their genomes and that there had been no recombination events.

Woods et al. discuss some clinical aspects of microcephaly but mainly focus on molecular and evolutionary factors.

From an evolutionary point of view, changes in genes linked to a microcephalic phenotype might have been responsible for the evolution of the human brain size.

Woods et al. also note that microcephaly is the consequence of a mitotic deficiency in neural precursors.

Microcephaly is caused by abnormal cell growth in the brain leading to a reduced brain size.

Mutations in genes involved in the cell cycle could be one factor causing this phenomenon.

Here, the authors showed that variations in brain size is more related to the number of connections between neurons.

See The Tragedy of the Commons.

This paper shows a link between grants and private-sector innovations and created a model to quantify the variation in funding for different fields.

Their results show an increase in private-sector patents by NIH.

In this article, the sociological expression "the rich get richer and the poor get poorer", also called Matthew effect, is presented in the context of scientific publication.

Scientists who have received grants in the past are more likely to get more grants and produce results.

This study applies an ethnic-name database to individual patent records granted by the United States Patent and Trademark Office to document these trends with greater detail than previously available.

The authors of this paper evaluated the impact of NIH grants on publications. They concluded that researchers who did not get an NIH grant but simultaneously applied for others grants saw one more publication (+7%).

This article is a reasonable hypothesis that preliminary data that contribute to receiving an outstanding peer review score likely lead to high visibility publications shortly after the grant is funded.

This article is about one negative effect of peer review, that an individual scientist devotes so much time and energy to getting financial support that it takes away from their science.

Basically, a huge disadvantage of the peer review program is that scientists must spend too much time writing what they intend to research, rather than performing the research.

The main goal of peer review in the biomedical sciences is to facilitate the introduction into medicine of improved ways of curing, relieving, and comforting patients. The achievement of this aim requires both quality control and the encouragement of innovation. If an appropriate balance between the two is lost, then peer review will fail to reach its purpose.

This study describes the advances in scientific knowledge and human health that have accrued as a result of the long-standing public investment in biomedical research.

Holbourn compared the head to a jar containing gelatin, hypothesizing that if the jar was shaken or violently rotated it would cause a shearing effect. He believed this shearing may be the culprit behind TBI.

Mott's investigation of "shell shock" in WWI veterans was the first human clinicopathological analysis of the physical effects of blast exposure on the brain.

The idea that an explosion could cause damage to the brain, and therefore potentially be responsible for mental deficits, led to a controversial national inquiry into blast exposure and veterans' health.

U.S. Department of Defense study that focused on blast-related lung injury and influenced thought behind blast-related injury for nearly half a century.

One of the first uses of a compressed gas shock tube to study blast exposure in an animal model.

A report of the long-term effects of repetitive head injury linked to American football.

An influential paper that drew national attention to mild TBI in military veterans.

A new naval history, or, Compleat view of the British marine... by John Entick was published in London in 1757.

This research examined 139 pairs of leaders and followers in the United States and Canada. What they found is that transformational leadership behaviors positively influence the environmental behavior of followers. "Transformational leaders" are trusted by followers because they have shown themselves to be experts, yet they make followers feel important too. Such leaders energize and empower followers to take on risks and to overcome challenges, trusting them to make good choices and feel confident about it. Perhaps surprisingly, transformational leadership is a teachable skill.

Schultz reviews the most common strategies for facilitating more sustainable behaviors. There are quite a variety of tools that can be employed, such as education, prompts, feedback, incentives, social norms, and public commitments. Which ones will prove most useful depends on how high or low the relative barriers and benefits are. This balance is affected by factors such as how challenging, novel, and (un)popular the new behavior is, how deeply ingrained the old habits are, and the relative likelihood of changing the context; for instance, infrastructure often takes a long time to change.

American decision-makers have procrastinated about making climate change–related policies because it is hard to see, feel, and understand the effects of climate change. These Yale University researchers use psychological research to describe how to engage people in the urgent task of reducing our climate impacts.

It is important to: highlight the local and personal impacts of a climate change, connect the proposed activity to behaviors that are already considered normal, highlight the benefits that people will gain, and tap into people’s emotions and values—including the sense of an ethical responsibility to other species, future humans, and the poor and marginalized.

Though the scientific community is in overwhelming agreement that climate change is a threat to human well-being, much of the public does not view the issue as a major risk.

In prior work, the "Cultural Cognition Thesis" proposes that this is because people form their ideas of risk by looking at how others in their identity groups perceive an issue. In contrast, the "Science Comprehension Thesis" proposes that it happens because people are not good at thinking like scientists.

Research by Kahan and colleagues finds support for the Cultural Cognition Thesis, but no evidence for the Science Comprehension Thesis.

Learn more at National Public Radio: http://www.npr.org/templates/story/story.php?storyId=124008307

This classic book reviews six key sources of persuasion:

1. Reciprocity: People feel compelled to return favors;
2. Commitment and consistency: People are more likely to agree to do something if they've agreed to something similar in the past;
3. Social proof: Especially in new situations, we watch what other people do and then copy it;
4. Authority: We do what a respected authority tells us to do;
5. Liking: We do what people we like do or tell us to do
6. Scarcity: We tend to be persuaded to do something if time is running out or if there's a risk that we might miss out.

This classic article describes what psychologists call "commons dilemmas." A commons dilemma occurs when individuals are tempted to overuse a shared resource.

In a commons dilemma, the immediate consequence benefits the individual, but the long-term consequence punishes the group.

These authors suggest that efforts to get people to behave sustainably are most successful when they harmonize with—rather than deny—our deeply embedded, evolutionary-based human tendencies. They identify five human tendencies and propose solutions that are consistent with them:

1. We are self-interested. Thus, emphasize benefits to people and their families.
2. We want to have more status than the people around us. Encouraging friendly competitions can increase motivation because people want to win.
3. We imitate others. Therefore, it is important to publicly display and communicate expected behavior.
4. We focus on the present. Thus, emphasize today's consequences.
5. We ignore what we can't sense. Therefore it is important to make the invisible visible.

Meta-analyses are "studies of studies," meaning that they look at patterns across a large number of research projects that focus on the same topic. This meta-analysis looked at data from 57 different samples. They conclude that psychological variables such as perceived control over a behavior, a sense of moral obligation to act, how difficult the behavior is, and whether their friends and family would support the behavior are connected to whether people intend to behave in pro-environmental ways. The intention to behave in pro-environmental ways, in turn, is the best predictor of actual pro-environmental behavior.

Another important feature of this article is that it replicates a previous meta-analysis completed 20 years ago and has consistent findings, meaning that even after 20 years, the patterns seem to be the same.

A research group at Yale University regularly measures the American public's views on climate change. People have a range of views from those who are extremely worried to those who dismiss climate change as not being real. The six categories are: alarmed, concerned, cautious, disengaged, doubtful, and dismissive. During the 2016 presidential election, only the alarmed group (17% of Americans) considered a candidate's position on climate change to be an important factor when deciding for whom to vote.

This article discusses how Traditional Ecological Knowledge (TEK) has helped indigenous groups maintain the biodiversity of their land and adapt to climate change. It contrasts TEK with more traditional quantitative experiments and suggests that the two approaches to understanding ecosystems can benefit from each other.

This book is the first to make the case that people who lead sustainability movements within organizations are most effective if they possess an ecologically accurate understanding of how the physical world works.

This article is the first major publication to apply the well-known psychological phenomenon called "pluralistic ignorance" to discussions about climate change.

Pluralistic ignorance is when people believe, inaccurately, that the person they are talking to might disagree with them, and decide not to speak up.

In the case of climate change, most Americans believe that it is occuring and that it is caused by humans, yet this research shows that people fail to speak up about climate change, believing that the person they are talking to might deny climate change exists.

This article addresses why people take political action about climate change. Researchers found that people are motivated to act only if they believe that a group effort by humans can reverse the course of climate change. Then, in order to act, people must believe that political actions such as calling elected officials and speaking up at meetings will have an impact on the governmental policies that impact climate change.

Bliuc and colleagues demonstrate that U.S. climate change worriers and skeptics hold very different social identities. These social identities have been formed around their opinion toward climate change (acceptance and concern vs. skepticism toward the science) rather than around demographic characteristics like religion or political party. The authors suggest that opinion about climate change has become a source of inter-group conflict similar to that surrounding the issues of abortion or same-sex marriage.

Psychologists have proposed for many years that human well-being increases when certain needs are fulfilled. Studies have explored basic physiogical needs, safety and security needs, social needs, and respect and autonomy needs. Little research, however, has examined whether these needs are common to all humans, or whether some of them are culture-specific.

Tay and Diener looked at the relationship between different kinds of needs and subjective well-being in 123 countries. They found evidence that all human beings share a variety of psychological and social needs in addition to basic needs.

This classic Science article examines Hardin's Tragedy of the Commons scenario with respect to global environmental commons such as oceans, freshwater, clean air, and the climate and atmosphere.

Dietz, Ostrom, and Stern suggest that it is difficult to govern global environmental commons because many of the features of historically successful commons management are missing at the global scale. These features include limiting access to the resource, monitoring resource use, promoting frequent face-to-face contact between users, and enforcing rules dictating resource use.

When it comes to our global environmental commons, the authors are guardedly optimistic that we can implement effective forms of governance and not over-exploit global natural resources.

Self-determination theory suggests that people are most motivated by situations that help them fulfill basic needs: autonomy, relatedness, and competence.

People need autonomy, to feel they have choices and are free to decide what, when, and how to proceed, rather than being forced by rules, deadlines, or evaluation by others. We seek relatedness, a sense of being socially connected and accepted by others. Competence is the need to accomplish an action with grace and achieve the desired outcome, as opposed feeling uninformed, or not having the requisite skills or abilities to achieve success.

This is a review article, organizing and summarizing what research has been conducted and suggests what future research should focus on.

Gifford and Nilsson review 18 factors that influence whether people behave in ways that help rather than hurt the environment. They organize the factors into two basic categories: personal and social.

The authors also recognize that people sometimes behave in pro-environmental ways because it is practical (such as saving money) and not because of these personal and social factors.

This article reviews how important it is for humans to maintain a connection with nature, especially when living in city environments. Research shows that our emotional and physical health improves when we engage with nature. There are many natural features that can be added to streets and buildings to facilitate keeping connected with nature including urban rivers, parks for play, and rooftop gardens.

Interesting process. I have tended to export all notes from one reference in a batch, and then organize them in DevonThink. In theory, this process is more efficient (I think) because I can process large numbers of notes in one go without constant app-switching. On the other hand, though, the method outlined is wonderfully direct: when you find information you need, you put it where you're going to need it.

Oh, hey, we know those guys. It's been a while since they've been mentioned in our readings, though.

This 2007 paper from Chiang et al. presented a new method for looking at the recruitment of different types of white blood cells to the site of an injury, while simultaneously identifying clusters of ligand-receptor couplings.

All of this can be visualized in live mice!

From this initial study, PSGL-1 was identified as a promising neutrophil ligand protein.

Goreau describes the species of corals found in Jamaica's reefs and the patterns of their distributions. He notes that the north and south coasts look different from each and hypothesizes that these differences are driven by differences in storm frequencies.

Connell describes a mechanism by which the high biodiversity of tropical rain forests and coral reefs is maintained by...

Severe tropical storms can cause widespread mortality in reef corals1,2. The Caribbean staghorn coral, Acropora cervicornis, although dependent on fragmentation for asexual propagation3–5, is particularly vulnerable to hurricane damage6,7. The most important agents of post-hurricane mortality are assumed to be high wave energy6 and change in salinity8, factors which typically soon diminish in intensity. We report here that there was substantial delayed tissue and colony death in A. cervicornis on a Jamaican reef damaged by Hurricane Alien. This previously undocumented degree of secondary mortality, sustained for 5 months and unrelated to emersion9, was over one order of magnitude more severe than that caused by the immediate effects of the storm. The elimination of >98% of the original survivors suggests potentially complex responses to catastrophes, involving disease10,11 and predation, which may explain the widely variable rates of reef recovery previously reported12–15.

Coral reefs on both the Pacific and Caribbean sides of Panama do not experience extreme weather events such as hurricanes. Coral diversity in Panama is maintained by mechanisms other than extreme weather disturbances, such as predation by the crown-of-thorns seastar, Acanthaster planci.

Researchers in Guam describe minimal damage to hard coral reefs after a typhoon and no long-term impact, even in exposed areas. This is likely due in part to the low, rugged profile of reefs in Guam.

Similarly to the reproducibility project in psychology, Errington and colleagues planned to conduct replication attempts on 50 important papers from the field of cancer biology. While the registered reports are already available online, the replication studies themselves are currently still being conducted.

Read more on eLife: https://elifesciences.org/collections/reproducibility-project-cancer-biology

Nosek and colleagues argue that scientists are often torn between "getting it right" and "getting it published": while finding out the truth is the ultimate goal of research, more immediately, researchers need to publish their work to be successful in their profession.

A number of practices, such as the establishment of journals emphasizing reports of non-significant results, are argued to be ill suited for improving research practices. To reconcile the two seemingly-at-odds motives, Nosek and colleagues suggest measures such as lowering the bar for publications and emphasizing scientific rigor over novelty, as well as openness and transparency with regard to data and materials.

John, Loewenstein and Prelec conducted a survey with over 2,000 psychologists to identify to which extent they used questionable research practices (QPRs). The respondents were encouraged to report their behavior truthfully, as they could increase donations to a charity of their choice by giving more truthful answers.

Results showed that a high number of psychologists admitted to engaging in QRPs such as almost 70% of all respondents admitting to not reporting results for all dependent measures, or around 50% of respondents admitting to reporting only studies that showed the desired results. Moreover, results showed that researchers suspected their peers also occasionally engaged in such QRPs, but that psychologists thought that there was generally no good justification for engaging in QRPs.

Fanelli assessed more than 2000 papers from different scientific disciplines and found that the proportion of studies reporting support for their hypotheses increased in the disciplines such as psychology or economics compared to disciplines such as space science. It is concluded that both the type of hypotheses tested and the rigor applied in these tests differ between fields.

Button and colleagues study the average statistical power of studies in neuroscience, and conclude that it is low. They highlight that low power does not only mean that studies have a lower chance of detecting a true effect, but that when using such low-powered studies, it is also becomes less likely that a significant effect indeed reflects a true effect. It is argued that using studies with low power may seem efficient at the first glance, because less money is spent on subjects, but that indeed, because future research could be building on an erroneous line of investigations, low-powered studies are inefficient in the long-run.

Hartshorne and Schachner suggest that replication success should be traced in a database connecting replication attempts with original studies. Based on this information, a replication success score could be computed, which could be used as a criterion for a journal's quality alongside other indicators such as citation counts.

Howard and colleagues examine how the file drawer problem affects a research literature. They compare "old", existing bodies of literature that could be suffering from the file drawer problem (i.e., which could include the few studies were an effect was found, while studies yielding non-significant results on the same effect were never published) with a newly constructed body of literature guaranteed to be free of the file drawer problem, which they achieved by conducting new studies. This investigation suggests that some bodies of literature are supported as relatively file-drawer-free, while other bodies of literature raise concern and kindle further studies on the effects they include.

Greenwald examines how research practices discriminate against accepting the null hypothesis (that an effect does not exist). Using a simulation, he suggests that too few publications accept the null hypothesis, and that the proportion of publications which falsely reject the null hypothesis although it would have been true is high.

Greenwald further debunks traditional arguments why a null hypothesis should not be accepted, and suggests ways to improve research practices to improve the acceptance of accepting the null hypothesis.

Simmons and colleagues conduct computer simulations and two experiments that show how significant results can easily be achieved for a research hypothesis that is false. They show that flexibility - or as they call it: researcher degrees of freedom - in four areas contributes to making it more likely to find significant effects for a false hypothesis:

1. Flexibility in choosing the dependent variables reported: When researchers flexibly analyze two related dependent variables, this already almost doubles the probability of finding a positive result for a false hypothesis. 2. Flexibility in choosing the sample size: When researchers stop data collection, find no significant result, and collect additional data before checking for the same effect, this increases the probability of finding a positive result for a false hypothesis by 50%.
2. Flexibility in the use of additional variables included in the analyses: When researchers include additional variables in the analyses, false positive rates more than double.
3. Flexibility in the number of experimental conditions reported: When researchers collect data in three experimental conditions and flexibly decide whether to report the result of comparisons between any two conditions or all three, this more than doubles the false positive rate.

If researchers used research practices where they used all four flexibilities, they would, overall, be more likely than not to find positive results although the underlying hypothesis was indeed false.

Rosenthal addresses the 'file drawer problem', a questionable research practice where only studies that showed the desired result would be published and all other studies would land in the 'file drawer' and would not be known to the scientific community.

In the extreme case, this could mean that, if a specific effect did not exist in reality, the 5% of studies that (due to statistical error allowed) find this effect get published and discussed as if the effect were true, whereas 95% of studies do not (and rightly so) find the effect, but are tucked away in a file drawer. This problem hinders scientific progress, as new studies would build on old, but false, effects.

Rosenthal introduces a way to assess the size of the file drawer problem, the tolerance to future null results: calculating the number of studies with null results that would have to be in a file drawer before the published studies on this effect would be called into question.

This study measured sunlight driven conversion of DOC to CO₂ in a lake in southern Finland. They measured lower quantum yields than the authors found in the paper you just read.

This line is from the Gospel of Mark.

This line is from the Chaldean Oracles.

This study presents an efficient method to produce neural stem cells from human pluripotent stem cells.

The system presented in this study enables the creation of NSC banks, increasing cell therapy applications.

This study examines the effects on the developing fetus of congenital cytomegalovirus infection.

In this study, Grief et al used electron microscopy to localize dengue virus in infected mosquito cells.

They concluded that the smooth membrane structures are an important site for the production of virus particles.

Tang’s article highlights the impact of ZIKV infection on both cell death and dysregulation of the cell cycle.

In this article, the authors were able to detect the Brazilian Zika virus in amniotic fluid and compare its genome to other Zika strains and flaviviruses. In doing so, they hoped to find out if there had been recombination events between them.

The authors collected amniotic fluid samples from women whose fetuses were diagnosed with microcephaly, extracted DNA purified virus particles, and analyzed the samples with qRT-PCR.

They found that the different viruses share 97–100% of their genomes and that there had been no recombination events.

Woods et al. discuss some clinical aspects of microcephaly but mainly focus on molecular and evolutionary factors.

From an evolutionary point of view, changes in genes linked to a microcephalic phenotype might have been responsible for the evolution of the human brain size.

Woods et al. also note that microcephaly is the consequence of a mitotic deficiency in neural precursors.

Microcephaly is caused by abnormal cell growth in the brain leading to a reduced brain size.

Mutations in genes involved in the cell cycle could be one factor causing this phenomenon.

Here, the authors showed that variations in brain size is more related to the number of connections between neurons.

This paper shows a link between grants and private-sector innovations and created a model to quantify the variation in funding for different fields.

Their results show an increase in private-sector patents by NIH.

In this article, the sociological expression "the rich get richer and the poor get poorer", also called Matthew effect, is presented in the context of scientific publication.

Scientists who have received grants in the past are more likely to get more grants and produce results.

The authors of this paper evaluated the impact of NIH grants on publications. They concluded that researchers who did not get an NIH grant but simultaneously applied for others grants saw one more publication (+7%).

This article is a reasonable hypothesis that preliminary data that contribute to receiving an outstanding peer review score likely lead to high visibility publications shortly after the grant is funded.

This article is about one negative effect of peer review, that an individual scientist devotes so much time and energy to getting financial support that it takes away from their science.

Basically, a huge disadvantage of the peer review program is that scientists must spend too much time writing what they intend to research, rather than performing the research.

Bruce Alberts, Marc W. Kirschner, Shirley Tilghman and Harold Varmus describe the advances in scientific knowledge and human health that have accrued as a result of the long-standing public investment in biomedical research.

• 5:48 Expert Political Judgment

  • Discusses the concept of Integrative Complexity
    • People with a lot of integrative complexity are more capable of reasoning about complex issues, distinguishing between facts and opinions, and seeing the world clearly as it is.
      • People who lack this quality tend to think in terms of black-and-white, and to have an arrogant and antagonistic attitude.
      • Fame is inversely correlated with integrative complexity

• 11:29 The Big Sort by Bill Bishop

  • There is an ongoing trend, especially on the Internet, but also geographically, for people to cluster based on their own worldview, while they become less and less open to different ideas.
    • The content filtering mechanisms of Tumblr and other social media websites, where you can simply unfollow whoever you disagree with, are the reason why this phenomenon is so prevalent on the Internet.

• 14:20 Pan's Labyrinth
  • Moral parable with "think for yourself; don't just blindly obey" as its message.

1. Robert Putnam - Bowling Alone, mentioned at 17:29

1A. Talks about the loss of community over time.

What's the source?

What's the source?

This part is quoted in a talk on the Thelemic concept of Holy Guardian Angel here.

This part is quoted in a talk on the Thelemic concept of Holy Guardian Angel here.

Some references made in this video:

• RISKS Digest
• A Ken'ichi who is a philosopher (his friend). ** The most likely match is Ken'ichi Sakemi, but I'm not sure.
• David J. Farber

This review was written by members of the same lab in which Dr. Roberson did the work described in this paper.

It outlines how the symptoms experienced by Alzheimer's patients seem to fluctuate constantly, suggesting that these symptoms cannot just be caused by dying neurons (which would result in symptoms that would get progressively worse).

The authors discuss known changes in other proteins in the brains of Alzheimer’s patients and how these protein networks might work together to mediate symptoms of Alzheimer’s disease in the brain.

Santa Cruz and colleagues studied genetically modified mice that had a mutation in the human version of the tau gene, which caused those mice to get tau tangles like those seen in Alzheimer’s disease.

Knocking out this tau gene allowed the mice to avoid memory and cognitive problems, although the tangles still formed.

Myers and colleagues examined patients that had died of progressive supranuclear palsy, a disease caused by a mutation in the tau gene.

They found that these patients also had an increased risk for Alzheimer’s disease, pointing to an important connection between tau and Alzheimer’s.

Tanzi and Bertram review the "amyloid hypothesis," which is the idea that a build-up of amyloid-β into plaques causes problems in tau, which then form tangles, causing the symptoms of Alzheimer’s disease.

This study was about mutations in the SLC9A6 gene, which are related with neurological diseases, such as X-linked mental retardation, microcephaly, epilepsy, and ataxia, a phenotype mimicking Angelman syndrome.

By using the experimental methods of linkage analysis and DNA sequencing they found out that a deletion in the SLC9A6 gene, encoding the Na(+)/H(+) exchanger NHE6, is basically responsible for these symptoms.

M. L. Jacquemont worked on the genetic heterogeneity of syndromic autism, more easily revealed through array-CGH. The author suggested that this method should be prioritized in order to diagnose autism. This study also revealed that patients with locus duplications are less affected that those presenting deletions. Finally, the importance of the chromosomal imbalance has no direct relation with the severity of the mental retardation.

Sebat and colleagues worked on the involvment of de novo Copy Number Variations in autism.

They showed that specific CNVs were mostly present in only one family among the tested group. They were also able to show the difference between simplex families, where autism is the result of spontaneous mutation and multiplex, where autism is most likely inherited.

Vorstman provides a review of much of the recent cytogenetic studies on autism. In these studies, researchers were able to identify abnormalities by looking at the shapes and sizes of chromosomes. From these observations, they were able to deduce if there were large-scale deletions, repetitions, or inversions in the chromosomes. A small percentage (about 3%) of autistic patients had mutations like this. Vorstman gathers these findings into one article and proposes regions scientists should focus on in future research.

P. Szatmari and colleagues have shown that copy number variants (CNV) were risk factors and causal events for autism. However, they are not the only parameters to be taken into account : oligogenic inheritance - inheritance of genes which, in a small quantity, code major changes - would be a prevalent factor of autism.

In this article, R. Canitano emphasizes the link between autism and epilepsy, showing that seizures are more frequent when mental retardation is associated with autism. The rate of comorbidity - cohabitation between two diseases, autism and epilepsy here - is estimated at 20-25%, meaning that this amount of autistic people is victim of seizures. This link has to be taken into account when considering therapy.

E. Fombonne has provided a review of epidemiological surveys on autism, in order to draw general conclusions. He concluded that autism is associated with mental retardation in about 70% of the cases and is overrepresented amongst males. He also showed that social class has no impact on the incidence of the disease. He also considered that available surveys did not allow to conclude that race or ethnicity influence the incidence of autism. Finally, no data could support the idea of secular evolution in the incidence of the disease.

Risch and colleagues studied the genetic makeup of subjects affected by autism.

They showed that autism is most likely caused by multiple genes and identified several genes that could play a part in this disease in different individuals.

This study was about the regulation of specific transcription factors by neuronal activity. They found out, by using techniques as mass spectrometry and chromatin immunopreuritation, that synaptic activity determines the expression of a set of neural gene products.

In this study also, a large nuclear protein, Cabin 1 (calcineurin-binding protein), was found out to be q cqlcium-regulated depressor of MEF2 activity.

This study was about a spontaneous mouse mutant, called slow-wave epilepsy (swe), which is related to several neurological syndromes, like ataxia, as well as about a unique epilepsy phenotype, that is characterized by 3/sec absence and tonic-clonic seizures.

swe was fine-mapped on Chromosome 4 and identified as a null allele of Nhe1, which is the Na+/H+ exchanger, a ubiquitous, and acts as an integral membrane protein involved in pH regulation. It removes intracellular acid, exchanging a proton for an extracellular sodium ion.

The aim of this study was to show the influence of two stimuli (produced in a short time sequence and called doublet) on the time where a tetanus was observed. By using single motor units of rats, it was shown that the doublet induced an increase of the tetanic tension and fusion. Also that slow motor units showed higher reaction to the doublet sensitivity than fast units.

Researchers took muscle samples from cats and tried different tetanus on them. They seem to have found the efficient pulse and frequencies by the motor neuron to generate a optimum muscle tension.

They investigated the evolution of the electric organs of eels. They looked at the DNA of the electric eels and two other species with electric organs. They detected many different genes for the developement of electric organs. Their results show that despite big differences in the electric cells of the investigates species, they have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs.

Some electrical fish produce not enough voltage to get an offensive or defensive meaning. In this study, authors try to understand in which this sorts of fish use this system. It will be demonstrate that it is used as direction and finding of the fish.

Effects of high‐frequency stimulation and doublets on dynamic contractions in rat soleus muscle exposed to normal and high extracellular

By recording firing pattern in motor units of rats, authors demonstrates quantitatively that, contractile properties of the muscular system is improve by the tree different respond allowed (fast but easily fatigued, slow but fatigue resistant, both). Also this paper in studying and recording the normal value of muscular contraction of an healthy rats, will allow the searcher to notice if is somethings wrong or interact with the motor control system. Like in our articles where the Eels's electricity make the muscular system of the fish goes off. "Firing patterns of motor units in normal rats"

The researchers investigated the behaviour of electric fish in french guiana. Notably, they describe in first the prey-capture behaviour of the electric eels.

Fish electric organs seams to be derived originally from muscle therefore a source of acetylcholine receptor. The Eels' anatomy was used many in different science domain such as Anatomy, embryology, and physiology. In previous research it was shown that the pathway between the nerve and electric organ used acetylcholine receptor. This is why this species, source of acetylcholine, conduct to very detailed studies by biochemist and neurologist.

"The Shocking History of Electric Fishes: From Ancient Epochs to the Birth of Modern Neurophysiology" is a book written by Stanley Finger and Marco Piccolino. In this study they follow different types of animal (flat torpedo rays, the electric catfishes, and the "eel" of our article). All three are able to produce electricity shocks and explain how they helped to change the sciences and medicine.

By studying the electroplaques of Torpedo-nobilian, the researcher try to understand how depolarising or hyperpolarizing changes in membrane potential occur. Furthermore they relief the latency time during stimulation of the nerve and the polarisation of the cells.

This study applies an ethnic-name database to individual patent records granted by the United States Patent and Trademark Office to document these trends with greater detail than previously available.

The main goal of peer review in the biomedical sciences is to facilitate the introduction into medicine of improved ways of curing, relieving, and comforting patients. The achievement of this aim requires both quality control and the encouragement of innovation. If an appropriate balance between the two is lost, then peer review will fail to reach its purpose.

This paper explored the role of β-catenin (protein involved in growth and thought to be a morphogen) which is expressed in the placode.

It was found that when this protein was mutated, the chickens would be scaleless(on the feet) and have abnormal feather growth.

The development of skin cells that give rise to hairs is reviewed in this paper.

A hair placode forms which allow for the expression of genes that determine skin cells and hair follicle development.

This paper proposed the theory that mammal hairs evolved from glandular structures. Whereas reptiles and birds skin (including feathers and scales) evolved a different pathway where a thick protective covering which would become scales.

This review deals with a model of how hair evolved, updating a model built in the 1972 (reference 3).

This model supposes that the development of hair was caused by mutations in patterning genes. this development allowed hair to become useful insulation.

This paper illustrates the way that crocodile head scales form. the process is different to the formation of other skin traits (such as feathers, hair and other scales).

The crocodile face and jaw scales are formed through the force of the growing cells physically pushing and cracking about hard shell forming unique patterns.

Chapter 10: Empathy, sympathy, and prosocial preferences in primates.

There are several potential lines of evidence for the existence of empathy in nonhuman primates. Because of the subjectivity in interpretation of animals' intentions as well as no defined assay for empathy or sympathy, "we cannot be certain whether any given interpretation is right or wrong."

"To transform singular observations of behavior into more robust findings we need to develop theoretically grounded hypotheses that we can subject to empirical testing."

http://www.amazon.com/Oxford-Handbook-Evolutionary-Psychology-Handbooks/dp/0199561788

"Current claims for the existence of empathy, sympathy, and moral sentiments and other-regarding preferences in other primates rest on an insecure empirical foundation.

The anecdotal accounts have limited value because they rely on subjective interpretation of animals' intentions and motivations and they are not systematically collected or analysed.

This means we cannot be certain whether any given interpretation is right or wrong and we have no means of discriminating against competing claims."

The chapter covering this controversial view of whether nonhuman animals display empathy may be found here:

http://www.amazon.com/Oxford-Handbook-Evolutionary-Psychology-Handbooks/dp/0199561788

Type the word empathy into the "search inside this book" window.

From materials and methods: Measuring opening style: Each door opening was classified to indicate how the door was opened.

Three types of opening were observed:

1) Rats opened the door by nudging it up with their head from the front of the restrainer (“head”),

2) rats opened the door by leaning on the heavy side of the door (“side”), or

3) rats opened the door by standing on top of the door (“top”).

This paper describes the patterns rodents take while exploring their environment using a computational method of analysis. SEE allows for the distinction between stopping and progressing, spatial spread, dynamics of space occupancy, number of stops per excursion, and the maximal speeds attained.

[http://www.sciencedirect.com/science/article/pii/S0149763401000227]

The authors tested whether albino rats could display altruistic characteristics. They defined altruism as "behavior of one animal that relieves another animal's 'distress.'"

The distress-causing paradigm was using a harness to suspend one rat free from the floor. The second rat is free in a separate compartment and can see and hear the suspended rat.

The second rat can bring the suspended rat down to the floor by pressing a lever, and did so significantly more than if there was a styrofoam block being suspended.

These results do point toward rats being capable of altruistic behavior because the rats performed an action that was not beneficial to itself, but that benefits one of its species.

These authors tested whether the purpose of pain expression is to attract comfort or receive aid from conspecifics.

For this they assayed the likelihood of a free mouse to approach/contact a jailed mouse experiencing pain versus a jailed mouse unaffected by pain.

This hypothesis was true in the case of female mice but not male mice. However the observer female mice only approached mice that were "known" (i.e., had previous contact with the observer mouse). Thus there is sex specificity to the social approach to pain in laboratory mice.

The contact made by the free mouse with the mouse in pain resulted in less pain behavior.

The authors of this paper measure the reaction one group of rats has to the outward show of pain of another rat receiving an electric shock.

One group of rats had lever pushing for food associated with the electric shock of another rat and a shock to themselves (paired shock). A second group had lever pushing for food associated with only themselves receiving a shock (unpaired shock). The third group received no shock when they pushed the lever for food (no shock).

The authors then measured the frequency of lever pushing by spectator rats from all three groups (paired shock, unpaired shock, and no shock) in response to shock delivery to the tester rat.

Rats trained in the paired shock paradigm reacted by significantly less lever pushing compared with the no shock group.

This suggests that the responses given by the paired shock group may be a result of conditioning rather than that action being a show of sympathy.

In this review, the authors note that "Empathy involves not only any sentimentally commanded encounters with another person’s actual or inferred emotional state but also some minimal recognition and understanding of another’s emotional state."

They also highlight the main components of empathy: shared neural representations, self-awareness, mental flexibility, and emotion regulation.

These components are used together to form a model to predict empathy deficits in social and neurological disorders.

de Waal et al.

The authors looked at consolation behavior in chimpanzees. Consolation is ranked under the same umbrella as empathy. In their paper it was defined as "an interaction in which an uninvolved bystander initiates friendly contact with a recent victim of aggression."

Main finding: The empathy hypothesis that states that consolation is more likely to occur among animals that are socially close was supported.

This is a very interesting paper showing that a single-nucleotide polymorphism in the BDNF gene can impair the extinction of a conditioned fear response in both humans and mice. This polymorphism is also associated with anxiety-related behavior and atypical frontoamygdala activity in humans.

This is important because it suggests that the variant allele may affect the efficacy of exposure therapy, which relies on the process of extinction.

The goal of this study was to examine the effects of chronic mild stress on hippocampal and medial prefrontal cortex potentiation and extinction memory in rats.

The authors found that chronic mild stress did not interfere with the extinction of fear, but did impair the recall of extinction.

They found that chronic mild stress interfered with the development of extinction-related potentiation in the hippocampal/medial prefrontal cortex pathway.

In this study, the BDNF gene was deleted from the hippocampi of mice. This impaired the animals' ability to recognize new objects, learn spatial orientation, and extinguish conditioned fear.

These cognitive impairments are also found in anxiety disorders, suggesting that BDNF in the hippocampus may play a role in anxiety and depression.

This is a very interesting article showing that BDNF, acting through the tyrosine kinase B receptor, is required for the consolidation of stable extinction memories.

This is an older paper that was one of the first to show that fear extinction may be an NMDA-dependent process by infusion an NMDA antagonist (AP5) into the amygdala and measuring fear potentiated startle.

This paper shows that infusion of CPP, which is an NMDA receptor antagonist, into the ventromedial prefrontal cortex can impair extinction recall.

Here, the authors review current research describing the role of BDNF in long-term potentiation, and its known molecular mechanisms.

In this paper, the authors examine how epigentic gene expression regulation of BDNF enables fear extinction.

This paper investigates the role of NR2-containing N-methyl-D-aspartate receptors in the ventromedial prefrontal cortex and lateral amygdala in the consolidation of fear extinction memories.

In this paper, the authors examine research that has led to the notion that the medial prefrontal cortex is a critical component in both emotional regulation and fear extinction.

How does the author estimate the number of elephants killed based on the weight of seized ivory?

It's known that only about 10% of all smuggled goods, such as ivory, drugs, or weapons, are caught by customs. So if 51 tons of seized ivory is only 10% of all poached ivory, the actual amount of all smuggled ivory should be 10 times as high, or about 510 tons (510,000 kilograms).

510,000 kg of ivory corresponds to about 51,000 elephants.

In this study the authors used improved methods to identify the geographic origin of the largest ivory seizure since the 1989 ivory trade ban. They showed that the ivory was from savanna elephants from a narrow east-to-west band of southern Africa, centered on Zambia.

The findings enabled law enforcement to focus their investigation to a smaller area and fewer trade routes. They also led the Zambian government to improve antipoaching efforts.

This earlier paper by the first author describes in greater detail how the genetic reference map was constructed. It also explains the statistical smoothing method that the authors used to assign a geographic location to seized ivory.

This paper shows that African elephants that live in forests are actually a different species than African elephants that dwell in the savanna. Until this paper, all African elephants had been grouped together as a single species.

The authors proposed two species names: Loxodonta africana for the savanna elephants and L. cyclotis for the forest elephants.

This document is produced by the United Nations Office on Drugs and Crime. It analyzes a range of key transnational crime threats and offers a view of its global dimensions.

This paper examined the long-term impact of poaching on elephant family structure, stress levels, and reproductive output approximately 15 years after the 1989 ivory ban was implemented. Before the ban, widespread poaching drastically altered the demographic structure of the African elephant family groups by decreasing the number of old adult female elephants.

The authors specifically examined 218 adult female African elephants from 109 groups that differed in size, age structure, and average genetic relatedness.

Females from groups that lacked an old matriarch, first-order relatives, and strong social bonds had significantly higher stress hormone levels than females from groups where these features existed. Female elephants from groups disrupted by poaching had significantly lower reproductive output.

The negative impact of poaching persisted 15 years after the 1989 ivory ban was implemented.

In this study, the authors demonstrated that drongos are heartless.

Melissa can edit as SitC

Findings from this study suggest that when juveniles are not engaged in supervised activities they are more likely to engage in certain anti-social behaviors; at the same time, the increase in interactions associated with school attendance leads to more interpersonal conflict and violence.

Using Census and FBI data, this study finds that schooling significantly reduces the probability of incarceration and arrest.

Controlling Crime considers alternative ways to reduce crime that do not sacrifice public safety. Among the topics considered here are criminal justice system reform, social policy, and government policies affecting alcohol abuse, drugs, and private crime prevention.

In this book, W. J. Wilson persuasively argues that problems endemic to America's inner cities--from fatherless households to drugs and violent crime--stem directly from the disappearance of blue-collar jobs in the wake of a globalized economy

This paper concludes that the most efficient strategy for strengthening the future workforce, both economically and neurobiologically, and improving its quality of life is to invest in the environments of disadvantaged children during the early childhood years.

A brief overview of research on the relationship between work and crime.

This study showed that unemployment and crime mutually influence one another over the individual's life span.

This and the subsequent reference discuss the concept of and the dangers associated with gene drives.

Gene drives are techniques that alter genes in such a way that biases their inheritance, making them spread more rapidly than normal through a population.

Mutagenic chain reaction is an example of a powerful gene drive method. They list several checkpoints that they recommend be completed before the use of gene drive in endogenous populations, such as designing and testing techniques for reversal of the gene drive and long term studies to fully understand the consequences of a gene drive strategy.

Describes how C4.4, a human GPI-anchored protein, was found.

Identifies hAG-2 and hAG-3 (nAG homologs) as ligands for C4.4, a GPI-anchored protein in humans.

hAG-2 (an nAG homolog in humans) is expressed alongside an estrogen receptor in breast-cancer cell lines. The authors propose that hAG may play some role in cancer.

Acetycholine, a neurotransmitter for skeletal muscle, was once thought to be a molecule crucial in limb regeneration. However, this paper shows that when its release is inhibited, the limb still regenerates.

Experiments showing the effects of Prod1 overexpression in regeneration are shown. Overexpression causes distal blastema cells to take on a proximal identity and disrupt proper limb patterning.

This paper shows how Prod1 was discovered in salamanders and provides a basis for this paper, as nAG is ligand.

A research article that shows that vitamin A causes issues with the PD axis during regeneration of salamanders. This paper provides the basis for using vitamin A and other retinoids to disrupt proper limb regeneration.

A good overview of limb regeneration, specifically in salamanders. Discusses some molecular mechanisms in regards to limb specification and muscle regeneration.

This article discusses the use of genetic profiling in tumors to determine the ideal course of treatment, something that has gained increasing attention as our sequencing technology improved.

This article provided evidence that p21 might play a role in the G2-M checkpoint in addition to its established role at the G1-S checkpoint.

Additionally, the paper looked at the protein Rb (retinoblastoma) and its role in checkpoint activation. Rb prevents cells from entering S phase when signals from growth factors are absent.

This paper showed that the levels of p21 normally oscillate throughout the cell cycle. However, in cells that did not have functional p53, no p21 was detected, implying that p21 expression is regulated by p53.

This paper discusses research on the process of centrosome duplication.

This paper established a role for p53 in the regulation of centrosomes, which enable the cell to separate its chromosomes during mitosis. Cells without functional p53 had abnormal numbers of centrosomes, leading to unequal chromosome segregation.

This paper looked at the role of the protein SMAD4 in a pathway called TGF-β signaling. The authors used homologous recombination to disrupt the SMAD4 gene.

This article investigated the G2-M checkpoint in irradiated colorectal cancer cells and found that p53 induced the expression of a protein called 14-3-3, which triggers G2 arrest.

This paper showed that mitotic checkpoints are often defective in cancer cells, leading to the chromosomal instability that may drive carcinogenesis (the development of cancer).

This paper described the protein geminin, which prevents DNA replication from occurring more than once per cell cycle. Geminin accumulates after DNA replication to block repeated replication, and it is degraded in mitosis so that the cell can replicate its DNA in the next S phase.

This article looked into the survival of different cell lines treated with radiation. The authors observed the appearance of "giant cells" that had undergone extra rounds of replication, which in turn generated multiple nuclei.

This paper showed that when cells lacking p21 were treated with DNA-damaging agents, they frequently underwent extra rounds of replication, which led to deformed nuclei and cell death.

This paper established a role for p21 in senescence, an age-dependent decline in the cell's ability to divide.

This paper showed that p21 functioned downstream of p53 in the activation of the G1-S checkpoint.

This review discusses what was known at the time about the regulation of the cell cycle and how we could potentially use this information to design new cancer drugs.

An early review of microglial origin in birds.

This study showed that invasion of embryonic tissue by yolk sac macrophages in zebrafish fails in the absence of macrophage colony-stimulating factor-1.

The authors of this study generated the RUNX1 fate mapping model used in this study and showed that yolk sac cells expressing Runx1 can develop into fetal lymphoid progenitors and adult hematopoietic stem cells (HSCs).

As shown in this paper, microglia are not affected by the autosomal recessive mutation osteopetrosis (op) that leads to a general skeletal sclerosis and decreased numbers of macrophages in various tissues.

A review of the role of the colony-stimulating factor-1, also known as macrophage stimulating factor, in immunity and inflammation.

This study suggested that microglia derive from yolk sac progenitors and actively proliferate in situ.

This study examines the origin and differentiation of dendritic cells.

A review of the developmental origins of hematopoietic stem cells and the molecular mechanisms that regulate lineage-specific differentiation.

In this review of the studies on the origins, phenotype, and function of embryonic phagocytes the authors conclude that yolk sac–derived macrophages constitute a separate lineage.

This study showed that limited recruitment of cells by the recipient in parabiotic models can be attributed to a short half-life of the donor-derived cells in the blood.

In this study the authors identified a unique population of peripheral Ly-6C(hi)CCR2(+) monocytes, which are preferentially recruited into the lesioned brain following irradiation.

Using parabiosis and irradiation in an experimental autoimmune encephalitis mouse model of multiple sclerosis, the authors found that peripheral monocytes infiltrate the brain and contribute to the progression of the disease but do not contribute to the pool of resident microglial cells.

Yet another early study supporting the hypothesis of microglial turnover via division and recruitment of peripheral monocytes into the brain parenchyma in the absence of the overt blood-brain barrier disruption.

One of the earlier studies of microglial origin, supporting their monocytic origin.

This is a comprehensive review of the ontogeny and functions of microglial cells.

Similar to this study, which showed that a young systemic factor could improve neurogenesis in old mice, Sinha et al. 2014 tested the same concept in muscle.

Exposure of GDF-11 in old mice led to improved muscle structure, restored genomic integrity in adult muscle stem cells, increased strength, and increased capacity for exercise.

This study, conducted in 1999, was one of the first to study the effects of age on brain networks. At the time, little was known about the relationship between age and brain mechanisms of changes in memory.

This study showed that age is related to changes in verbal memory, and not picture memory.