Playing with proteins in virtual reality.

Much of my mental effort while I was doing laboratory research on the mechanisms of visual transduction (changing light into a nerve signal in our retinal rod and cone photoreceptor cells) was devoted to trying to visualize how proteins might interact with each other. I spent many hours using molecular model kits of color-coded plastic atoms one could plug together with flexible joints, like the Tinkertoys of my childhood. If I had only had the system now described by O'Connor et al! Have a look at the video below showing manipulating molecular dynamics in a VR environment,  and here is their abstract:

We describe a framework for interactive molecular dynamics in a multiuser virtual reality (VR) environment, combining rigorous cloud-mounted atomistic physics simulations with commodity VR hardware, which we have made accessible to readers (see isci.itch.io/nsb-imd). It allows users to visualize and sample, with atomic-level precision, the structures and dynamics of complex molecular structures “on the fly” and to interact with other users in the same virtual environment. A series of controlled studies, in which participants were tasked with a range of molecular manipulation goals (threading methane through a nanotube, changing helical screw sense, and tying a protein knot), quantitatively demonstrate that users within the interactive VR environment can complete sophisticated molecular modeling tasks more quickly than they can using conventional interfaces, especially for molecular pathways and structural transitions whose conformational choreographies are intrinsically three-dimensional. This framework should accelerate progress in nanoscale molecular engineering areas including conformational mapping, drug development, synthetic biology, and catalyst design. More broadly, our findings highlight the potential of VR in scientific domains where three-dimensional dynamics matter, spanning research and education.

Sampling molecular conformational dynamics in virtual reality from david glowacki on Vimeo.

Increasing despair among poor Americans.

A survey by Goldman et al. of more than 4,600 American adults conducted in 1995-1996 and in 2011-2014 suggests that among individuals of low socioeconomic status, negative affect increased significantly between the two survey waves, and life satisfaction and psychological well-being decreased:

Significance

In the past few years, references to the opioid epidemic, drug poisonings, and associated feelings of despair among Americans, primarily working-class whites, have flooded the media, and related patterns of mortality have been of increasing interest to social scientists. Yet, despite recurring references to distress or despair in journalistic accounts and academic studies, there has been little analysis of whether psychological health among American adults has worsened over the past two decades. Here, we use data from national samples of adults in the mid-1990s and early 2010s to demonstrate increasing distress and declining well-being that was concentrated among low-socioeconomic-status individuals but spanned the age range from young to older adults.

Abstract

Although there is little dispute about the impact of the US opioid epidemic on recent mortality, there is less consensus about whether trends reflect increasing despair among American adults. The issue is complicated by the absence of established scales or definitions of despair as well as a paucity of studies examining changes in psychological health, especially well-being, since the 1990s. We contribute evidence using two cross-sectional waves of the Midlife in the United States (MIDUS) study to assess changes in measures of psychological distress and well-being. These measures capture negative emotions such as sadness, hopelessness, and worthlessness, and positive emotions such as happiness, fulfillment, and life satisfaction. Most of the measures reveal increasing distress and decreasing well-being across the age span for those of low relative socioeconomic position, in contrast to little decline or modest improvement for persons of high relative position.

A fundamental advance in brain imaging techniques.

I want to pass on the abstract, along with a bit of text and two figures, from an article by Coalson, Van Essen, and Glasser that argues for a fundamental change is how functional cortical areas of the brain are recorded and reported.  They demonstrate that surface based parcellation is 3-fold more accurate than traditional volume based parcellations.:

Significance

Most human brain-imaging studies have traditionally used low-resolution images, inaccurate methods of cross-subject alignment, and extensive blurring. Recently, a high-resolution approach with more accurate alignment and minimized blurring was used by the Human Connectome Project to generate a multimodal map of human cortical areas in hundreds of individuals. Starting from these data, we systematically compared these two approaches, showing that the traditional approach is nearly three times worse than the Human Connectome Project’s improved approach in two objective measures of spatial localization of cortical areas. Furthermore, we demonstrate considerable challenges in comparing data across the two approaches and, as a result, argue that there is an urgent need for the field to adopt more accurate methods of data acquisition and analysis.

Abstract

Localizing human brain functions is a long-standing goal in systems neuroscience. Toward this goal, neuroimaging studies have traditionally used volume-based smoothing, registered data to volume-based standard spaces, and reported results relative to volume-based parcellations. A novel 360-area surface-based cortical parcellation was recently generated using multimodal data from the Human Connectome Project, and a volume-based version of this parcellation has frequently been requested for use with traditional volume-based analyses. However, given the major methodological differences between traditional volumetric and Human Connectome Project-style processing, the utility and interpretability of such an altered parcellation must first be established. By starting from automatically generated individual-subject parcellations and processing them with different methodological approaches, we show that traditional processing steps, especially volume-based smoothing and registration, substantially degrade cortical area localization compared with surface-based approaches. We also show that surface-based registration using features closely tied to cortical areas, rather than to folding patterns alone, improves the alignment of areas, and that the benefits of high-resolution acquisitions are largely unexploited by traditional volume-based methods. Quantitatively, we show that the most common version of the traditional approach has spatial localization that is only 35% as good as the best surface-based method as assessed using two objective measures (peak areal probabilities and “captured area fraction” for maximum probability maps). Finally, we demonstrate that substantial challenges exist when attempting to accurately represent volume-based group analysis results on the surface, which has important implications for the interpretability of studies, both past and future, that use these volume-based methods.

Some context from their introduction:

The recently reported HCP-MMP1.0 multimodal cortical parcellation (https://balsa.wustl.edu/study/RVVG, see the graphic below) contains 180 distinct areas per hemisphere and was generated from hundreds of healthy young adult subjects from the Human Connectome Project (HCP) using data precisely aligned with the HCP’s surface-based neuroimaging analysis approach. Each cortical area is defined by multiple features, such as those representing architecture, function, connectivity, or topographic maps of visual space. This multimodal parcellation has generated widespread interest, with many investigators asking how to relate its cortical areas to data processed using the traditional neuroimaging approach. Because volume-registered analysis of the cortex in MNI space is still widely used, this has often translated into concrete requests, such as: “Please provide the HCP-MMP1.0 parcellation in standard MNI volume space.” Here, we investigate quantitatively the drawbacks of traditional volume-based analyses and document that much of the HCP-MMP1.0 parcellation cannot be faithfully represented when mapped to a traditional volume-based atlas.

Here is a graphic from the parcellation analysis

And here is Figure 1 and its explanation from the Coalson et al. paper.

The figure shows a probabilistic maps of five exemplar areas spanning a range of peak probabilities. Each area is shown as localized by areal-feature–based surface registration (Lower, Center), and as localized by volume-based methods. One area (3b in Fig. 1) has a peak probability of 0.92 in the volume (orange, red), whereas the other four have volumetric peak probabilities in the range of 0.35–0.7 (blue, yellow). Notably, the peak probabilities of these five areas are all higher on the surface (Figure, Lower, Center) (range 0.90–1) than in the volume, indicating that MSMAll nonlinear surface-based registration provides substantially better functional alignment across subjects than does nonlinear volume-based registration.

Mindfulness training increases strength of right insula connections.

Sharp et al.(open source) suggest that:

The endeavor to understand how mindfulness works will likely be advanced by using recently developed tools and theory within the nascent field of brain connectomics. The connectomic framework conceives of the brain’s functional and structural architecture as a complex, dynamic network. This network view of brain function partly arose from the lack of support for highly selective, modular regions instantiating specialized functions. That is, large meta-analyses consisting mostly of univariate fMRI analyses disconfirm that, for example, the amygdala is exclusively selective for fear processing. Indeed, more fruitful mechanistic knowledge of how neural systems function may emerge from delineating how different regions communicate functionally across a range of environments, and by identifying the underlying structural connections that constrain such functional dynamics.

Their abstract, and a summary figure:

Although mindfulness meditation is known to provide a wealth of psychological benefits, the neural mechanisms involved in these effects remain to be well characterized. A central question is whether the observed benefits of mindfulness training derive from specific changes in the structural brain connectome that do not result from alternative forms of experimental intervention. Measures of whole-brain and node-level structural connectome changes induced by mindfulness training were compared with those induced by cognitive and physical fitness training within a large, multi-group intervention protocol (n = 86). Whole-brain analyses examined global graph-theoretical changes in structural network topology. A hypothesis-driven approach was taken to investigate connectivity changes within the insula, which was predicted here to mediate interoceptive awareness skills that have been shown to improve through mindfulness training. No global changes were observed in whole-brain network topology. However, node-level results confirmed a priori hypotheses, demonstrating significant increases in mean connection strength in right insula across all of its connections. Present findings suggest that mindfulness strengthens interoception, operationalized here as the mean insula connection strength within the overall connectome. This finding further elucidates the neural mechanisms of mindfulness meditation and motivates new perspectives about the unique benefits of mindfulness training compared to contemporary cognitive and physical fitness interventions.

Legend - Anatomical representation of tractography pathways between right insula and highly connected regions. Connections displayed (only corticocortical, here) comprised the top 80% connection strengths across all insula pathways. (A) Displays pre-training connections in right insula, which showed the greatest structural reorganization across mindfulness training. (B) Represents the same image as in (A) except at post-training.

Mortality rates level off at extreme age

Interesting work from Barbi et al. showing that human death rates increase exponentially up to about age 80, then decelerate, and plateau after age 105. At that point, the odds of someone dying from one birthday to the next are roughly 50:50. This implies that there might be no natural limit to how long humans can live, contrary to the view of most demographers and biologists.:

Theories about biological limits to life span and evolutionary shaping of human longevity depend on facts about mortality at extreme ages, but these facts have remained a matter of debate. Do hazard curves typically level out into high plateaus eventually, as seen in other species, or do exponential increases persist? In this study, we estimated hazard rates from data on all inhabitants of Italy aged 105 and older between 2009 and 2015 (born 1896–1910), a total of 3836 documented cases. We observed level hazard curves, which were essentially constant beyond age 105. Our estimates are free from artifacts of aggregation that limited earlier studies and provide the best evidence to date for the existence of extreme-age mortality plateaus in humans.

Brain imaging predicts who will be a good musical performer.

Fascinating observations from Zatorre's group:

Significance

In sophisticated auditory–motor learning such as musical instrument learning, little is understood about how brain plasticity develops over time and how the related individual variability is reflected in the neural architecture. In a longitudinal fMRI training study on cello learning, we reveal the integrative function of the dorsal cortical stream in auditory–motor information processing, which comes online quickly during learning. Additionally, our data show that better performers optimize the recruitment of regions involved in auditory encoding and motor control and reveal the critical role of the pre-supplementary motor area and its interaction with auditory areas as predictors of musical proficiency. The present study provides unprecedented understanding of the neural substrates of individual learning variability and therefore has implications for pedagogy and rehabilitation.

Abstract

The auditory and motor neural systems are closely intertwined, enabling people to carry out tasks such as playing a musical instrument whose mapping between action and sound is extremely sophisticated. While the dorsal auditory stream has been shown to mediate these audio–motor transformations, little is known about how such mapping emerges with training. Here, we use longitudinal training on a cello as a model for brain plasticity during the acquisition of specific complex skills, including continuous and many-to-one audio–motor mapping, and we investigate individual differences in learning. We trained participants with no musical background to play on a specially designed MRI-compatible cello and scanned them before and after 1 and 4 wk of training. Activation of the auditory-to-motor dorsal cortical stream emerged rapidly during the training and was similarly activated during passive listening and cello performance of trained melodies. This network activation was independent of performance accuracy and therefore appears to be a prerequisite of music playing. In contrast, greater recruitment of regions involved in auditory encoding and motor control over the training was related to better musical proficiency. Additionally, pre-supplementary motor area activity and its connectivity with the auditory cortex during passive listening before training was predictive of final training success, revealing the integrative function of this network in auditory–motor information processing. Together, these results clarify the critical role of the dorsal stream and its interaction with auditory areas in complex audio–motor learning.

Why are religious people trusted more?

A prevailing view is that religious behavior facilitate trust, primarily toward coreligionists, and particularly when it is diagnostic of belief in moralizing deities. Moon et al. suggest a further reason that religious people are viewed as more trustworthy than non-religious people: they follow 'slow life-history' strategies that tend to be sexually restricted, invested in family, nonimpulsive, and nonaggressive, all traits that associated with cooperativeness and prosociality. They find that direct information about life history reproductive strategy (i.e., a subject's “dating preferences”) tend to override the effects of religious information. Their abstract:

Religious people are more trusted than nonreligious people. Although most theorists attribute these perceptions to the beliefs of religious targets, religious individuals also differ in behavioral ways that might cue trust. We examined whether perceivers might trust religious targets more because they heuristically associate religion with slow life-history strategies. In three experiments, we found that religious targets are viewed as slow life-history strategists and that these findings are not the result of a universally positive halo effect; that the effect of target religion on trust is significantly mediated by the target’s life-history traits (i.e., perceived reproductive strategy); and that when perceivers have direct information about a target’s reproductive strategy, their ratings of trust are driven primarily by his or her reproductive strategy, rather than religion. These effects operate over and above targets’ belief in moralizing gods and offer a novel theoretical perspective on religion and trust.

Seven creepy Facebook patents

I'll follow yesterday's post with yet another post on creepy high tech patents, this time from Facebook, showing their ongoing intention to invade our privacy as much as possible. From the article by Chinoy:

Reading your relationships

One patent application discusses predicting whether you’re in a romantic relationship using information such as how many times you visit another user’s page, the number of people in your profile picture and the percentage of your friends of a different gender.

Classifying your personality

Another proposes using your posts and messages to infer personality traits. It describes judging your degree of extroversion, openness or emotional stability, then using those characteristics to select which news stories or ads to display.

Predicting your future

This patent application describes using your posts and messages, in addition to your credit card transactions and location, to predict when a major life event, such as a birth, death or graduation, is likely to occur.

Identifying your camera

Another considers analyzing pictures to create a unique camera “signature” using faulty pixels or lens scratches. That signature could be used to figure out that you know someone who uploads pictures taken on your device, even if you weren’t previously connected. Or it might be used to guess the “affinity” between you and a friend based on how frequently you use the same camera.

Listening to your environment

This patent application explores using your phone microphone to identify the television shows you watched and whether ads were muted. It also proposes using the electrical interference pattern created by your television power cable to guess which show is playing.

Tracking your routine

Another patent application discusses tracking your weekly routine and sending notifications to other users of deviations from the routine. In addition, it describes using your phone’s location in the middle of the night to establish where you live.

Inferring your habits

This patent proposes correlating the location of your phone to locations of your friends’ phones to deduce whom you socialize with most often. It also proposes monitoring when your phone is stationary to track how many hours you sleep.

A patent for emotional robots?

I recently received an interesting email from Deepak Gupta, who is with a patent research services company, who, having seen my post on robots and emotion, thought to point me to a description of a patent application filed by Samsung. It seems so straightforward that I would have thought that such a patent would have been proposed years ago. It is an attempt to get past the "uncanny valley" issue, the feelings of eeriness and revulsion people can have in observing or interacting with robots. (It still seems a bit scary to me.)

...an electronic robot includes a motor mounted inside its head. A head part of the robot consists of a display unit, to display emotional expressions and a motor control unit that can rotate the robot’s head in a clockwise or counter-clockwise direction on its axis.

The electronic robot decides which emotional expression to be displayed on a display panel by sensing information from its various sensors, such as a camera sensor, a pressure sensor, a geomagnetic sensor, and a microphone to sense the motion of a user. Accordingly, the electronic robot tracks the major feature points of the face such as eyes, nose, mouth, and eyebrows from user images captured by the camera sensor and recognizes user emotional information, based on basic facial expressions conveying happiness, surprise, anger, sadness, and sorrow. Once the information is received from the sensors, the data is then analyzed by the processor that sends an appropriate voltage signal to the display unit and the motor control unit in order to express relevant emotion. The emotional states expressed by the electronic robot include anger, disgust, sadness, interest, happiness, impassiveness, surprise, agreement (i.e., “yes”), and rejection (i.e., “no”).

To express emotional states, the electronic robot stores motion information of the head predefined for each emotional state in a storage unit. The head motion information includes head motion type, angle, speed (or rotational force), and direction.

The technology disclosed in the patent document allows robots to express emotions. Therefore, these robots can communicate or interact with humans more effectively. These robots can be used in the applications that require interaction with humans, for instance, communicating with patients in a hospital in the absence of actual staff, or even interacting with pets such as dogs or cats that are left alone by their owners during their working hours.

An optimistic outlook creates a rosy past.

From Devitt and Schacter in the Harvard Psychology department, a study recruiting the usual gaggle of psychology undergraduate students as subjects:

People frequently engage in future thinking in everyday life, but it is unknown how simulating an event in advance changes how that event is remembered once it takes place. To initiate study of this important topic, we conducted two experiments in which participants simulated emotional events before learning the hypothetical outcome of each event via narratives. Memory was assessed for emotional details contained in those narratives. Positive simulation resulted in a liberal response bias for positive information and a conservative bias for negative information. Events preceded by positive simulation were considered more favorably in retrospect. In contrast, negative simulation had no impact on subsequent memory. Results were similar across an immediate and delayed memory test and for past and future simulation. These results provide novel insights into the cognitive consequences of episodic future simulation and build on the optimism-bias literature by showing that adopting a favorable outlook results in a rosy memory.

Stress and autoimmune disease

I am now in my 77th year, and not all that pleased that my inflammatory, immune, and stress systems are becoming more excitable, more likely to be activated by small environmental perturbations that went unnoticed 10 or 20 years ago. Increases in sympathetic nervous system and inflammatory process with aging have been documented in many studies, and there is a literature linking stress with immune system dysfunction at all ages. This post points to yet another study of the linkage of stress with immune system activity. Song et al. report a massive study of over one million people in a Swedish cohort over a thirty year period that shows a strong association between persons suffering stress disorders and increased risk of developing autoimmune diseases such as arthritis and Crohn's disease. This affirms the strong link between psychological stress and physical inflammatory conditions. Here is a truncated and edited statement of results from the JAMA paper:

The median age at diagnosis of stress-related disorders was 41 years, and 40% of the exposed (i.e. suffering from stress-related disorder) patients were male. During a mean follow-up of 10 years, the incidence rate of autoimmune diseases was 9.1, 6.0, and 6.5 per 1000 person-years among the exposed, matched unexposed, and sibling cohorts, respectively. Compared with the unexposed population, patients with stress-related disorders were at increased risk of autoimmune disease... Persistent use of selective serotonin reuptake inhibitors during the first year of posttraumatic stress disorder diagnosis was associated with attenuated relative risk of autoimmune disease.

Social media and democracy

This post passes on links to articles on social media discussed recently in the Univ. of Wisconsin Chaos and Complex Systems seminar that I attend. (Two previous MindBlog posts have noted Jaron Lanier's critique of social media, "Ten arguments for deleting your social media accounts right now," which coins an acronym, BUMMER, for what Lanier considers one of its core evils. BUMMER is “Behaviors of Users Modified, and Made Into an Empire for Rent.”)  I want to point now to Franklin Foer's review of Lanier's book (Foer claims he actually deleted his Facebook account after reading the book. I haven't managed to do that.)

As an antidote to the current pessimism about the social effects of social media, Ethan Zuckerman offers an essay "Six or seven things social media can do for democracy." He takes his title from an article by Schudson, “Six or Seven Things News Can Do for Democracy,” that anchored his book, "Why Democracies Need an Unloveable Press." Schudson's list of functions for journalism or news is to inform, investigate, analyze, be a public forum, be a tool for social empathy, be a force for mobilization, and promote representative democracy.

Zukerman makes a similar list for the functions of social media, that I condense here:
1. Social media can inform us. (Arab Spring, Ferguson Missouri) but also misinform us (fake news, pizza parlor prostitution ring.)
2.   Social media can an amplify important voices and issues (which might either strengthen or weaken democracy)
3. Social media can be a tool for connection and solidarity (of either good or evil groups, pro or anti democratic.) 
4. Social media can be a space for mobilization (Tahrir Square, Taksim Gezi Park, Charlottesville, pro or anti-democratic.)
5. Social media can be a space for deliberation debate (yet also disappointing, mean, petty, superficial, uncivil.)  There needs to be more effort to build civil platforms.
6. Social media can show us diversity of views and perspectives.    (However, bubbles, homophily, racism, ethnonationalism, can inhibit this).  Conscious intervention is needed change this.
7. Social media can be a model for democratically governed spaces.   Social platforms should seek, be based on consent of their communities. (Example of Reddit, ~1000 volunteer moderators, rules, policing of rule breakers.)

One of Zuckerman's concluding paragraphs   

Finally, it’s also fair to note that there’s a dark side to every democratic function I’ve listed. The tools that allow marginalized people to report their news and influence media are the same ones that allow fake news to be injected into the media ecosystem. Amplification is a technique used by everyone from Black Lives Matter to neo-Nazis, as is mobilization, and the spaces for solidarity that allow Jen Brea to manage her disease allow “incels” to push each other towards violence. While I feel comfortable advocating for respectful dialog and diverse points of view, someone will see my advocacy as an attempt to push politically correct multiculturalism down their throat, or to silence the exclusive truth of their perspectives through dialog. The bad news is that making social media work better for democracy likely means making it work better for the Nazis as well. The good news is that there’s a lot more participatory democrats than there are Nazis.

The Philosophy we need: Personalism

To his credit, David Brooks keeps searching for moral visions that might be an antidote to our current social and political malaise. A recent Op-Ed piece is on Personalism, the:

...philosophic tendency built on the infinite uniqueness and depth of each person. Over the years people like Walt Whitman, Martin Luther King, William James, Peter Maurin and Wojtyla (who went on to become Pope John Paul II) have called themselves personalists, but the movement is still something of a philosophic nub.

...our culture does a pretty good job of ignoring the uniqueness and depth of each person. Pollsters see in terms of broad demographic groups. Big data counts people as if it were counting apples. At the extreme, evolutionary psychology reduces people to biological drives, capitalism reduces people to economic self-interest, modern Marxism to their class position and multiculturalism to their racial one. Consumerism treats people as mere selves — as shallow creatures concerned merely with the experience of pleasure and the acquisition of stuff.

..personalism is a middle way between authoritarian collectivism and radical individualism. The former subsumes the individual within the collective. The latter uses the group to serve the interests of the self.

Personalism demands that we change the way we structure our institutions. A company that treats people as units to simply maximize shareholder return is showing contempt for its own workers. Schools that treat students as brains on a stick are not preparing them to lead whole lives.

The big point is that today’s social fragmentation didn’t spring from shallow roots. It sprang from worldviews that amputated people from their own depths and divided them into simplistic, flattened identities. That has to change. As Charles Péguy said, “The revolution is moral or not at all.”

Mindfulness can lower your motivation.

Vohs and Hafenbrack do an NYTimes opinion piece to advertise their forthcoming paper on effects of meditation. Given my personal experience with 'mindfulness' I think they are right on track. Some clips:

The practical payoff of mindfulness is backed by dozens of studies linking it to job satisfaction, rational thinking and emotional resilience...But on the face of it, mindfulness might seem counterproductive in a workplace setting. A central technique of mindfulness meditation, after all, is to accept things as they are. Yet companies want their employees to be motivated. And the very notion of motivation — striving to obtain a more desirable future — implies some degree of discontentment with the present, which seems at odds with a psychological exercise that instills equanimity and a sense of calm.

To test this hunch, we recently conducted five studies, involving hundreds of people, to see whether there was a tension between mindfulness and motivation...Among those who had meditated, motivation levels were lower on average. Those people didn’t feel as much like working on the assignments, nor did they want to spend as much time or effort to complete them. Meditation was correlated with reduced thoughts about the future and greater feelings of calm and serenity — states seemingly not conducive to wanting to tackle a work project...previous studies have found that meditation increases mental focus, suggesting that those in our studies who performed the mindfulness exercise should have performed better on the tasks. Their lower levels of motivation, however, seemed to cancel out that benefit...Mindfulness is perhaps akin to a mental nap. Napping, too, is associated with feeling calm, refreshed and less harried. Then again, who wakes up from a nap eager to organize some files?

Mindfulness might be unhelpful for dealing with difficult assignments at work, but it may be exactly what is called for in other contexts. There is no denying that mindfulness can be beneficial, bringing about calm and acceptance. Once you’ve reached a peak level of acceptance, however, you’re not going to be motivated to work harder.