The terms congruence and incongruence are used in the 2nd and 3rd core conditions in Person-Centred Therapy.

Carl Rogers developed PCT, and outlined in a Journal of Consulting Psychology (1957) that 6 core therapeutic conditions are needed for constructive personality change and that all 6 must be present in therapy. Rogers considered that no other conditions are necessary.  The 6 core conditions are:

2 people are to be in psychological contact
The client is to be incongruent
The therapist is to be congruent or integrated in the relationship
The therapist experiences Unconditional Positive Regard (UPR) for the client
The therapist has empathetic understanding of the client’s internal frame of reference and endeavours to communicate the empathy to the client
The communication to the client of the therapist’s empathy and UPR is to a minimum degree achieved.

Incongruence
This term used in the 2nd core condition refers to a discrepancy between the client’s perception and the reality of the situation.  The client will be aware of the reality but perceives it differently.

It refers to a discrepancy between the actual experience of the organism and the self picture of the individual insofar as it represents that experience… [An] instance would be the mother who develops vague illnesses whenever her only son makes plans to leave home. The actual desire is to hold on to her only source of satisfaction. To perceive this in awareness would be inconsistent with the picture she holds of herself as a good mother.  (Rogers, 1957, p. 2)

Congruence
This term used in the 3rd core condition refers to the exhibition of genuineness, transparency and wholeness.  The therapist will not give perceptions of professionalism which disguises the humanity of the therapist.  However, the therapist will convey any feelings of confusion, dislike or any other feelings arising within themselves through advanced empathy, in order to be transparent and genuine.

  Can I be real in the relationship?  This has come to have an increasing amount of importance to me over the years.  I feel that genuineness is another way of describing the quality I would like to have.  I like the term congruence by which I mean that what I am experiencing inside is present in my awareness and comes out through my communication.  In a sense, when I have this quality, I am all in one piece in the relationship. (Rogers, et al., 1965)

 -- Edit to clarify more as requested in comments --

The situation with the mother in Rogers' example shows that the mother sees her ideal self to be a good mother but her perception of her self image is that she is not a good mother as she develops vague illnesses whenever her son plans to leave home.

References

Rogers, C., 1957. The Necessary and Sufficient Conditions of Therapeutic Personality Change. [Online]
Available at: http://www.shoreline.edu/dchris/psych236/Documents/Rogers.pdf
[Accessed 15 March 2016]

Rogers, C., Perls, F. & Ellis, A., 1965. Video: Three approaches to psychotherapy. [Online]
Available at: https://www.youtube.com/watch?v=SgiX0QLnpBM
[Accessed 15 March 2016].


Anxiety vs Stressfulness in the Big Five?

Your question indicates that your research indicates a close association between stress and anxiety. I've tried a few different approaches to separating these terms but with limited success.  Investigation included a review of:

Concomitant literature
Biological associations
Personality disorders
Lexical relatedness
Concomitant therapies

Concomitant literature
The Journal of Anxiety, Stress & Coping is dedicated to anxiety and stress, which indicates that they are very closely related topics.  The aims of the journal include:

understanding of the relationship between psychological and physiological processes during stressful and anxious states

Google scholar identifies over 3 million articles concurrently including stress and anxiety, indicating some level of association or correlation.
Biological associations

Stress and anxiety appear to be associated in heart disease (Chauvet-Gelinier & Bonin, 2017).

Neuropeptides have been identified that concurrently relate to stress and anxiety (Heilig, 2004; Cohen, 2012).

Personality disorders
The Diagnostic and Statistical Manual of Mental Disorders (DSM-5), lists the adjustment disorders (page 286) concurrently with stress and anxiety.  Interestingly, the DSM lists the word 'stress' 237 times and 'anxiety' 1280 times.
Lexical
The Oxford and Collins dictionary lists anxiety and stress as synonyms.  Merriam Webster lists them as near synonyms.
One definition of synonym is that you can use two words interchangeably in a sentence without loss or alteration of meaning.
Anxiety and stress are both abstract nouns and emotions, being able to be used in the sentence:  "I feel a sense of anxiety" and "I feel a sense of stress".
The curators of the Oxford and Merriam Webster dictionaries appear to believe that anxiety and stress are closely associated.
My own research is in the lexical analysis of personality, emotion and behaviour (Mobbs, 2020).  The words stressed and anxious can be visualised as follows.  It is visually apparent that the terms are highly related, possibly synonyms.  The question mentions Big-5; both anxious and stressed are in the region of the atlas denoted by the Big-5's neuroticism dimension.

Therapies
A range of therapies appear to be targeted at concurrently dealing with stress and anxiety, such as:

Group therapy (White, 1992)
Talk therapy,
Cognitive behavioral therapy (Hopkinson, 2019)
Dialectical behavior therapy (Fitzpatrick, 2019)
Music therapy (Umbrello, 2019)
Physical exercise (Mikkelsen, 2017)

References
Chauvet-Gelinier, J. C., & Bonin, B. (2017). Stress, anxiety and depression in heart disease patients: A major challenge for cardiac rehabilitation. Annals of physical and rehabilitation medicine, 60(1), 6-12.
Mikkelsen, K., Stojanovska, L., Polenakovic, M., Bosevski, M., & Apostolopoulos, V. (2017). Exercise and mental health. Maturitas, 106, 48-56.
White, J., Keenan, M., & Brooks, N. (1992). Stress control: a controlled comparative investigation of large group therapy for generalized anxiety disorder. Behavioural and Cognitive Psychotherapy, 20(2), 97-113.
Hopkinson, M. D., Reavell, J., Lane, D. A., & Mallikarjun, P. (2019). Cognitive behavioral therapy for depression, anxiety, and stress in caregivers of dementia patients: A systematic review and meta-analysis. The Gerontologist, 59(4), e343-e362.
Fitzpatrick, S., Bailey, K., & Rizvi, S. L. (2019). Changes in Emotions Over the Course of Dialectical Behavior Therapy and the Moderating Role of Depression, Anxiety, and Posttraumatic Stress Disorder. Behavior Therapy.
Umbrello, M., Sorrenti, T., Mistraletti, G., Formenti, P., Chiumello, D., & Terzoni, S. (2019). Music therapy reduces stress and anxiety in critically ill patients: a systematic review of randomized clinical trials. Minerva anestesiologica, 85(8), 886-898.
Heilig, M. (2004). The NPY system in stress, anxiety and depression. Neuropeptides, 38(4), 213-224.
Cohen, H., Liu, T., Kozlovsky, N., Kaplan, Z., Zohar, J., & Mathé, A. A. (2012). The neuropeptide Y (NPY)-ergic system is associated with behavioral resilience to stress exposure in an animal model of post-traumatic stress disorder. Neuropsychopharmacology, 37(2), 350-363.
Mobbs, A. E. (2020). An atlas of personality, emotion and behaviour. PloS one, 15(1), e0227877. https://doi.org/10.1371/journal.pone.0227877


Are there "6 degrees of separation" for ideas?

You are asking two different questions in your title and the text. I will answer the text question, explain why you are asking two different questions, and comment on the title question.

The human mind seems to have some sort of relational structure for how it works with ideas. This is usually study in the domain of memory via free recall. In a free recall experiment, a participant will memorize a list of items and then be asked to recall them in any order. Alternatively, there might be no list to memorize and instead the participant may be asked to name as many of some common things as they can quickly (for instance: name all the animals you know). The experimenter tracks the time delays between recall of items, and uses that to infer the "mental distance" between concepts.

It a typical experiment, you will see clustering effects with participants quickly naming a bunch of objects of one type before taking slightly longer to transition to another type and then name many objects of that type quickly. As an example, I might be asked to name cartoon characters and I would start listing:

  "Bart" [short delay] "Homer" [short delay] "Marge" [short delay] "Lisa" [short delay] "Maggie" [long delay while my mind switches from 'The Simpsons' cluster to 'Futurama' cluster] "Fry" [short delay] Leela [short delay] Dr. Zoidberg [etc]

This suggests that I naturally connect and infer different relationships between ideas. In particular, the temporal structure of my recall reveals that I known concepts like "The Simpsons" and "Futurama" and I connect certain names to each other because they share a relationship of "being on the same show". Of course, how I structure my categories and recall is shaped by my expertise.

As an experimenter, I could represent the way people structure their ideas as a graph/network, with individual ideas represented as nodes and closely related ideas (or ones between which people usually transition often or quickly) connected by edges. Free recall is then a random walk on this network. The netwok is similar to a social network, except there nodes are people and edges exist between friends. However, just because what you are studying has a network structure, doesn't mean that it has "6 degrees of separation".

The "6 degrees of separation" idea is a subset of all networks that are known as small-world networks. Small-world networks are defined as networks on $n$ nodes where the longest shortest path (i.e. the fewest edges you need to follow to get from any arbitrary node to any other arbitrary node) is of length about $\log n$. Many networks, say a regular grid, are not small-world (in the case of the regular grid, the length of the longest shortest path is proportional to $\sqrt{n}$ which is much bigger than $\log n$). Thus, the question in the body of you post is not necessarily related to the title.

However, if we take a highly clustered small-world network and perform a random walk on it, then the results will be similar to what we see in free recall experiments. In particular, the random walk will tend to wander for a while in one cluster until taking a jump to another cluster where it would again linger. Thus, the relational structure of ideas might be consistent with small-world networks.


How does the brain compute sound localisation without the equations?

Some neuroscience papers on sound localization:

Joris Philip X, Smith Philip H, and Yin Tom C.T Coincidence Detection in the Auditory System // Neuron (1998)
Agmon-Snir Hagai, Carr Catherine E. and Rinzel John The role of dendrites in auditory coincidence detection // Nature (1998)
Trussell Laurence O. Synaptic mechanisms for coding timing in auditory neurons // Annual Review of Physiology (1999)
Grothe B., Pecka M., & McAlpine D. Mechanisms of Sound Localization in Mammals // Physiological Reviews (2010)
Chen X, Leischner U, Rochefort NL, Nelken I, Konnerth A. Functional mapping of single spines in cortical neurons in vivo // Nature (2011)

Books

Blauert, J.: Spatial hearing: the psychophysics of human sound localization; MIT Press (1983)
Schnupp, Nelken and King: Auditory Neuroscience: Making Sense of Sound, MIT Press, 2011


How to efficiently use a statistical consultant?

This is a challenging question. As a bit of background, I am a cognitive scientist for the most part (by my highest graduate degree), but in addition to that, I have graduate degrees in both math and statistics and I have worked professionally as a consultant in those fields for many years. So I have some access to the problems on both sides of this question.

Statistical consulting is a point of training for some, but certainly not all, graduate students in statistics. What this means is that some people acting as consultants will be well trained in this activity, while others may be picking it up as they go. So you want to talk to either a more senior consultant or work with a statistics consultancy that has more senior people there to make sure your consultant knows what he or she is doing. That said, there is a standard of care in consulting these days, outlined in (among other examples) this ASA document, this 2010 conference paper, and this white paper by Flavia Jolliffe. Also Zahn and Isenberg is a classical paper on this. These may give you an idea of what the consultants who get trained are taught.

Consultants in statistics are well trained (usually!) in methodologies, but the main weakness in their training is usually exposure to the complexities of any given scientific field. In particular, unless they consult for people in your field regularly, the single hardest problem will be communicating in a concise way what it has taken you years to learn yourself: the specifics of your research problems. A solution here is to find someone who specializes in problems related to your research area. While not comprehensive, this page at ASA lets you search for statisticians by speciality, including some content areas (including epidemiology). Also remember that statisticians live in various academic departments (if you are using academic consultants) and these departments often are only vaguely aware of each other: as an example, I used to be at a university where the main campus statistical consultancy was in a school of social sciences, and the actual statistics department did not interact with them at all. Searching broadly is sometimes helpful.

If you cannot find a specialist, then communication is the key, and it will take longer to get to results in your relationship with your consultant. The paper by Jolliffe (above) has good advice that might be useful both to the consultant and to the client in terms of what to do and how to communicate (and there are some references there that go further). But this will be the central problem, so working closely on clarifying the research goals is probably the most important step.

A good preparation is to think about the problem before meeting the consultant and imagine trying to explain it to a good student or colleague from another field. Try to think through the particularly specialist parts of the problem before meeting the consultant; how would you explain these to someone new in your research lab? Likewise, if the consultant is not clear in responding to you, be direct is asking for more clarity. I believe this is covered by item E.2 of the ASA's ethical guidelines for consulting and collaborating for statisticians.

Not that any of this applies to your case, but from the point of view of the consultant, there are a number of things worth noting. First, clients, especially those with statistical knowledge, often come in with strong expectations of what the right answer is, and sometimes grow offended at questions from the consultant that try to get at the real questions being asked. As an example, I used to consult with psychologists who basically wanted me to tell them how to do an ANOVA on their data, even when that was the wrong analysis. So be open to analyses that you are not used to using. Also, a good consultant will ask a lot of questions to clarify the statistical question you want answered. Always assume good faith, and do try to answer the questions even if you don't fully understand them. But be willing to say (and explain) when you think the consultant's questions miss the point. Another issue is when people come into consulting so late that all there is for the statistician to do is conduct a post mortem. If you are serious about consulting, meet with them early on in the process. Finally, work out payments or collaboration rules up front. You would be amazed how often statisticians are asked to do pro bono work, either implicitly or explicitly.

tl;dr Communication, and it may take some time.


Confidence rating in cognitive experiments

If the question is 'Will it start to rain based on this cloud cover?' and the answer is a binary 'yes' or 'no' and the subsequent question is 'How sure are you about that?', then the answer to your question

  Does the confidence rating reflect their estimate of likelihood of
  rain, or rather the likelihood that the choice is correct?

is the latter: it reflects the likelihood that the choice is correct, because when they say 'no it will not rain', with a confidence of 60%, then the chance it will rain is 40% and not 60%. Hence, it reflects the confidence they have in their answer.


Can a self-paced-reading & grammaticality judgment task be programmed in PsychPy or Open Sesame?

Disclaimer - I'm a big fan of, and occasional contributor to, OpenSesame.

Yes, but you can't expect anyone here to do it for you.
I would recommend using OpenSesame for this, as you'll need to use Python, and OpenSesame makes this side of things easier for beginners.
My advice is to head over to the website, take a look at the documentation there, have a go yourself, and use the forum there to ask for help in specific points.

I will say though, that it's much better to attempt to design the experiment yourself and ask for help, rather than looking for someone to do it for you. The OpenSesame people really appreciate that!


Yes but it is referred to as Disruptive Mood Dysregulation Disorder in DSM 5 and is characterized by persistent irritability and frequent episodes of extreme, out-of-control behavior.


Is there any empirical support evaluating the fast phobia cure?

Witkowski has written several articles reviewing NLP (2010, 2012) and in each case has found few studies that indicate clear support for the technique. He also argues that the articles which indicate no support for NLP are generally of stronger methodological quality than those which do not. The fast phobia cure is not directly mentioned in either paper.

Jemmer (2005) provides an overview of the fast phobia technique, and describes a handful of studies which have used and reported on it; you may find his paper to be a starting point for identifying information on the technique, although it seems most of the studies he cited are in the NLP database and it is unclear if they have been published in peer review journals. Jemmer's article acknowledges the lack of evidence, and is primarily written from a theoretical perspective.

A 2011 review identified three peer-reviewed studies and 1 dissertation that examined NLP techniques for phobia and reported the techniques to be effective (Biswal & Prusty). The review does not go into detail as to the exact NLP techniques used in these studies but this may be a source of literature for further reading. Biswal and Prusty (2011) also highlight some of the theoretical issues which have hampered NLP research and provide a helpful overview distinguishing some of NLP's techniques from other psychotherapeutic techniques.

A 2012 review examined 10 peer-reviewed NLP studies which were either randomized controlled trials or pre-post designs, 3 of which assessed fast phobia techniques (Sturt et al.). Some effects were found in terms of decreased fear or anxiety, but these generally occurred in all treatment groups (not just NLP) or in studies with no control group. Most outcomes were self-report measures. However, these studies may be the most relevant to your initial question.

Overall, the consensus of these reviews indicates that there is little evidence to support the use of NLP in general, including the fast phobia cure. However, the studies also note that the lack of high quality research may indicate more rigorous studies are needed before discarding the NLP concept entirely. Additionally, the reviews point out that several NLP phobia techniques are similar to other psychotherapy techniques for treating phobia, so there may be stronger evidence for those subcomponents elsewhere in the literature. These reviews should provide a good starting point and working vocabulary if you are interested in researching those subcomponents.

Biswal, R., & Prusty, B. (2011). Trends in neuro-linguistic programming (NLP): A critical review. Social Science International, 27(1), 41-56.

Jemmer, P. (2005). Phobia: Fear and loathing in mental spaces. European Journal of Clinical Hyponosis, 6(3), 24-32.

Sturt, J., Ali, S., Robertson, W., Metcalfe, D., Grove, A., Bourne, C., & Bridle, C. (2012). Neurolinguistic programming: A systematic review of the effects on health outcomes. British Journal of General Practice, November, e757-e764.

Witkowski, T. (2010). Thirty-five years of research on neuro-linguistic programming. NLP Research Database. State of the art or pseudoscientific decoration? Polish Psychological Bulletin, 41(2), 58-66.

Witkowski, T. (2012). A review of research findings on neuro-linguistic programming. The Scientific Review of Mental Health Practice, 9(1), 29-40.


How to create an online test of bias using preference judgements on pairs of pictures?

To answer your general question, many psychology experiment delivery systems, and even general programming languages could be used to present a set of trials where participants provide responses regarding pairs of visual stimuli.
In particular, I've found Inquisit to be a good option if you want to deliver the experiment online.

If you examine the task library you can find examples of IAT and GNAT studies which involve pairs of stimuli in order to estimate implicit bias. If you look around you should be able to find some examples involving visual stimuli.


Why doesn't the brain get into infinite loops when being queried?

The brain often does create looping conditions. When these loops involve a large number of neurons, we call it a seizure. An analogy in electrical engineering would be a feedback loop -- such as literal feedback between a microphone and speakers. In the brain, fortunately, these loops are usually self-dissolving since the neurons involved will often run out of neurotransmitter or energy, or inhibitory neurons will get involved (like referees breaking up a fight). Many of the neurotransmitters and hormones in the body act as regulators of ongoing processes. There are almost always negative feedback mechanisms whose purpose is to prevent overload on various systems. The equivalent in programming would be using a counter variable in a while loop to break if it loops too many times.

This all, of course, was with respect to short pathways (small number of links). Larger, more complex pathways such as thoughts and goals are probably handled in part by different mechanisms, such as the instinct of not wanting to waste too much time getting nowhere. At the same time, getting frustrated and rage quitting is a perfect example of hormones and neurotransmitters rising to the point of stopping the loop of trying to do something that is not working as desired.


Latency between actual neurons firing and muscles response in open and close fist experiment

Short answer
Reported motor delays between brain activity and motor response are in the order of 6 - 9 ms.

Background
I found a study where the authors used deep brain stimulation electrodes implanted in the subthalamic nucleus (STN, Fig. 1) in patients with Parkinson's disease to activate motor tracts at a subcortical level. The STN is not part of the pyramidal motor system, but is thought to keep things in check. Stimulation in Parkinson's is used to control involuntary movements. In this study, the authors activated motor tracts at a subcortical level via the STN (Costa et al, 2007)

The authors recorded facial, cervical and upper limb muscle responses bilaterally by means of motor-evoked potentials (MEPs) in the trapezius, deltoid, biceps and thenar muscles as well as the orbicularis oculi, orbicularis oris, masseter and sternocleidomastoid muscles. They report mean latencies in the range 6.0 - 9.1 ms. MEP latencies in the orbicularis oculi and orbicularis oris were significantly longer than in the masseter and sternocleidomastoid.

In your experiments, there was direct, voluntary activation of the motor pathway via the pyramidal system in (healthy?) subjects. In contrast, the cited study recorded latencies in Parkinson's sufferers after direct electrical activation of a subcortical structure. Hence, the pathway is different between the two studies and the latencies observed in the cited study may not apply fully to your data set. Nonetheless, it may help you to narrow the time window in which you might search for the brain activity relative to the motor output from the experimental glove.

Fig. 1. Overview of a brain slice showing the position of the STN. source: Wikipedia

Reference
- Costa et al., Brain. (2007); 130(1): 245-55


Why is Potassium(K) important to neurology & the brain?

The main cell of the brain is the neuron. The neuron has a semipermeable membrane that under specific circumstances lets potassium through. Another common cell is the glia cell, which only has potassium channels. Potassium, K+, has a positive charge and it can pass across the membrane at specific channels, depending on their state (open/closed). The channels are ion specific as the amino acids that make up the channels (proteins) have different charges and configurations.

Different membrane ion channels have different roles. K+ is mainly found in the cytoplasm during resting state with an equilibrium potential of -75mV. In the typical neuron model, this potential is larger than that of Na+ or Cl-.

Ions seek out an equilibrium where they do not have to move because positive and negative charges repel each other. However, the cell is determined to manage this laziness and to avoid a stand-still, it has a negative potential.

When K+ exits the cell, the relationship between positive and negative ions changes, leading to an increasing voltage difference between the inner cytoplasmic and the outer extracellular ions. The negativity in the cell increases and two things happen: a chemical driving force from K+ and an electrical driving force - resulting from the voltage difference. As the K+ exits the cell, neighboring channels increasingly adopt the same pattern and this gives rise to a domino effect along the cell membrane, which travels through the axon. As this switch from -/+ to +/- occurs as K+ passes the membrane the outer charges ++++ switch to ----. This results in a voltage +- that grows along the axis ++--, +++---, ++++----, but this is mediated by Cl-, resulting in a cycling of the potential - and it moves:

------, +-----, ++----, +++---, +++++-, -+++++, --++++, ---+++, ----+, ------

(Kandel et al., Principles of Neural Science, 5th ed., p.126-129, p.144)

The potassium drives the action potential and that is why neurons can "talk to each other" and signals can reach their destination. This is why potassium is important for the nervous system.

Above, +++--- implies the outer charge and thus the cell membrane has the voltage:

+ + + - - -
- - - + + +


Can people with absolute pitch identify the exact frequency, or simply the pitch class?

Short answer
In practice, absolute pitch is generally tested for by using musical pitch classes.

Background
Absolute pitch (AP) is the ability to identify the pitch of a musical tone, or to produce a musical tone at a given pitch without the use of an external reference pitch. Most humans process musical pitch relatively rather than absolutely, and in fact most sensory systems operate relatively and not absolutely. AP is indeed a rare ability, occurring in less than 0.01% of the general population (Tekuechi & Hulse, 1993).

The way in which AP is tested is mostly using pitch classes. Pitch classes are likely preferably used experimentally, because people with AP are often musicians. Musicians are already familiar with pitch classes because of their training. In turn, AP typically manifests itself in trained musicians (Zatorre, 2003). Therefore, testing AP using frequencies expressed in Herz may simply be too abstract for most people with AP, since they are more accustomed to the use of pitch classes.

Note that, because the pitch A4 used to tune orchestras, corresponds to 440.0 Hz by modern convention, AP as tested with pitch classes can be, indirectly, considered to represent frequencies.

Some subjects with AP may consistently identify pitches a semitone low or a semitone high. This can occur because a subject may be accustomed to a different tuning standard for A4 than 440.0 Hz (Tekuechi & Hulse, 1993). Hence, AP has a strong correlate to training.

References
- Tekuechi & Hulse, Psychol Bull (1993); 113(2): 345-61
- Zatorre, Nature Neurosci (2003); 6(7): 692-5


Could Fitts Law be used to measure difficulty in platform genre games?

Probably, though my brief literature search didn't turn up any examples of people actually measuring game difficulty using Fitts' law. One thing to keep in mind is that motor movements are only a portion of what might make a game physically or cognitively demanding, even in platform games which are typically quite simple. Users have to make additional decisions, such as which platform to jump to or where to attend (do I look at the platform I'm jumping to, or do I look ahead to anticipate the next jump?)

I did find one interesting paper by Looser, Cockburn, & Savage (2005), who use Fitts' law to predict movement time in first-person shooters. The authors found that the time taken to pan (using a mouse) to acquire a target could be accounted for by Fitts' law. So if the time to acquire a target (e.g. before an enemy starts shooting at you) is critical, it certainly suggests that your methodology could be used to moderate difficulty level, say, by placing enemies farthest away from the current position.

Again, this is mostly speculation as I don't think there are any actual studies that address your specific question. But your intuition seems quite reasonable.

  Looser, J., Cockburn, A., & Savage, J. (2005). On the validity of
  using First-Person Shooters for Fitts' law studies. Proceedings of.
  People and Computers XIX, 2, 33-36. PDF


Does this rdists package provide actual (predicted) response time for each observation?

Not very familiar with this package, but per manual (bold and italics added):

  ddiffusion gives the density, pdiffusion gives the distribution function, qdiffusion gives the quantile function (i.e., predicted RTs), and rdiffusion generates random response times and decisions (returning a data.frame with columns rt (numeric) and response (factor)).

So, it looks like if you want predicted reaction times, you should use the qdiffusion function (but note that it is a quantile function).


Effect of time on emotion self-perception

As shown in the Wikipedia section "Memory of felt emotion" there are many ways that recollected emotion is significantly different than experienced emotion. From the section:

  Another study found that people's memories for how distressed they
  felt when they learned of the 9/11 terrorist attacks changed over time
  and moreover, were predicted by their current appraisals of the impact
  of the attacks (Levine et al., 2004). It appears that memories of past
  emotional responses are not always accurate, and can even be partially
  reconstructed based on their current appraisal of events. [45]

  Studies have shown that as episodic memory becomes less accessible
  over time, the reliance on semantic memory to remember past emotions
  increases. In one study Levine (2009)[47] primes of the cultural belief
  of women being more emotional than men had a greater effect on
  responses for older memories compared to new memories. The long term
  recall of emotions was more in line with the primed opinions, showing
  that long term recall of emotions was heavily influenced by current
  opinions.

  [45] Levine L.J. and Pizarro D.A. (2004) "Emotion and memory research:
  A grumpy overview" Social Cognition, Vol. 22, No. 5, 2004, pp.530-554

  [47] Levine; Lench, Heather; Safer, Martin (2009). "Functions of
  Remembering and Misremembering Emotion". Applied Cognitive Psychology.
  23: 1059–1075.


How do animals recognize other animals of their own species?

The obvious: animals use a variety of senses

There's a wikipedia article on intra-species recognition. The article states:

  Different species may employ different methods, but all of them are
  based on one or more senses (after all, this is how the organism
  gather information about the environment). The recognition may happen
  by chemical signature (smell), by having a distinctive shape (sight),
  by emitting certain sounds (hearing), or even by behaviour patterns.
  Often a combination of these is used....
  Intra-species recognition systems are often subtle...
  Sometimes, too, intra-species recognition is fallible

Of course, this is all fairly obvious, true, and not that helpful.

A few articles of possible relevance

Mateo (2004) has a review of recognition systems in animals if you want a more general theoretical framework.
Pfennig (1998) discusses intra-species recognition and the relationship with mate selection.

Musings on your particular question

In your particular example of two cars driving along with windows closed, we are probably excluding senses of smell and sound and requiring the dogs to rely exclusively on sight.
I wonder whether prototype theory or some other human visual categorisation theory would apply to dogs also?

References

Mateo, J. (2004). Recognition systems and biological organization: the
perception component of social recognition. In Annales Zoologici
Fennici, volume 41, pages 729-745.
PDF
Pfenning (1988) PDF

I'm way outside my expertise here. I tossed up whether to post this at all. I figured I'd post in the absence of another answer a week after posting. The above represents what I found from a little research.


Trying to understand equations in Karl Friston article

As mentioned in the definitions section on page 2 of the paper, $D(q||p) = <ln(q/p)>_q$ is the Kullback-Leibler divergence or cross-entropy between two densities.

The reason for the negative logs is that is the convention when discussing entropy in the context of information theory.  This allows information to be combined additively. (https://en.wikipedia.org/wiki/Entropy_(information_theory)#Rationale)


Impaired verbal communication, but normal reading and writing skills?

Just a reminder that Stack Exchange is not an appropriate place to get a diagnosis; a vague description of symptoms may indicate a variety of possible outcomes.  See a doctor instead.  That said:

One general term for disorders that affect some language modalities and not others, when the cause is psychological rather than physical (ie, not deafness, muscle weakness, paralysis, etc), is aphasia:

  To be diagnosed with aphasia, a person's speech or language must be
  significantly impaired in one (or several) of the four communication
  modalities following acquired brain injury or have significant decline
  over a short time period (progressive aphasia). The four communication
  modalities are auditory comprehension, verbal expression, reading and
  writing, and functional communication.

Aphasia is most commonly associated with stroke or dementia, and several sub-types involve both speech production and verbal comprehension difficulties, while not necessarily affecting reading or writing abilities.

Other diagnoses are also possible, as language disorders may consist of a combination of a variety of possible aspects of language ability, while not affecting others.  For example, children with both receptive (comprehension) and expressive (speech) delays may be diagnosed with specific language impairment (SLI):

  ... diagnosed when a child's language does not develop normally and
  the difficulties cannot be accounted for by generally slow
  development, physical abnormality of the speech apparatus, autism
  spectrum disorder, apraxia, acquired brain damage or hearing loss.

Though relatively rarely, it is possible for literacy to be largely unaffected by SLI.

Additionally, comorbidity is also possible, such as a combination of speech agnosia and apraxia, and if other symptoms are present, then yet other diagnoses would apply, such as autism, where again, it is possible for some language skills (such as verbal communication) to be impaired while others (such as literacy) are largely unaffected.

For a general overview of the field, see speech and language impairment and communication disorder.  A summary of technical terminology used to classify symptoms can be found here.


Biological Plausibility of Back-Prop

No, the algorithm of back-prop (BP) isn't biologically plausible. However, there are other means which involve propagating the error through multiple layers of neurons in a feed-forward network which are biologically plausible. But before we evaluate these substitutions, let's review why back-prop isn't biologically plausible [1]:

1. Weight Transport Problem

BP uses the same weights for forward-pass and backward error propagation. But synapses are uni-directional.

2. Derivative Transport Problem

The derivative of each neuron is used to modulate the error signal in BP. Additionally, the derivative is propagated through each layer. How this derivative calculated by neurons and then propagated, is unclear.

3. Linear Feedback Problem

The BP feedback path is linear, but neurons aren't linear.

4. Spiking Problem

Neurons spike. BP is defined for rates.

5. Timing Problem

The BP error signal is expected to propagate instantaneously. Calculations and signal transmission in the brain do not happen instantaneously.

6. Target Problem

Most applications of BP rely on many examples with given labels, but where do those labels come from?

Replacements for Back-Prop

Most replacements for back-prop solve a subset of these problems, however none of them see to solve all of them. In "Spiking Deep Neural Networks: Engineered and Biological Approaches to Object Recognition", a method is constructed using the NEF that solves all problems except for the Target Problem. This means there are no replacements for BP that work for all cases where BP is applied, which is to be expected given this is what usually happens when biological plausibility is emphasized.

Beyond Back-Prop

However, it should be noted that there is more than back-propagation through fully-connected networks involved in Deep Learning. Specifically, the are a number of different architectures used, such as Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs).

CNNs aren't biologically plausible due to their reliance on weights being exactly equal across multiple locations.
RNNs rely on Back-Propagation Through Time (BPTT), of which there is currently no biologically plausible analogue [2].

This confusion between Deep Learning, neural network architectures and back-prop is reason that Yann LeCunn is trying to get people to adopt the term "Differentiable Computing" instead of "Deep Learning". At which point, the question must shift from "Is Deep Learning biologically plausible?" into "What aspects of Differentiable Computing are biologically plausible?" Which is much harder to answer, but at least we have a better question than when we started!

[1] Summarized from Eric Hunsberger's PhD Thesis "Spiking Deep Neural Networks: Engineered and Biological Approaches to Object Recognition"

[2] That being said, there are other means of learning (supposedly) biologically plausible recurrent neural network weights (FORCE training, Conceptors), however they don't resemble BPTT in any way. The discussion of these methods is outside the scope of this question.


The article "Vector reconstruction from Firing Rates" of Abbott and Salinas

What they mean is that as long as you rotate $C_i$ and $C_j$ by the same amount, the dot product will be the same.  This is rotational invariance because the dot product is invariant to coherent rotation of the relevant vectors.

In neural terms, the correlation between the activity of two neurons (in a population representing a one dimensional circular variable) is a function of the difference in their preferred orientations and does not depend on the absolute direction of their orientations.


Predictive Experiments on Neuroscience of Free Will

There is a good article on Wikipedia on the Neuroscience of Free Will, with far too much content to adequately summarize here.  Since your question is focused on long-term prediction of behaviour, I'll just mention about that.

Using newer fMRI technology, Soon et al (2008) used a learning algorithm to predict "free will" decisions from brain activity about 7 seconds (and up to 10 seconds) prior to the subject reporting awareness of having made the decision.  This experiment has been replicated in other labs: Presenter Marcus du Satoy undergoes it for the BBC documentary The Secret You (2009/2010), and remarks that there is something creepy about the radiologist being aware of his decision several seconds before even he is.

An important question remains regarding all long-term prediction experiments: Human behaviour is very predictable, as countless experiments in every area of psychology commonly demonstrate by manipulating causal factors - the ability to predict it well in advance with significant accuracy is hardly limited to neuroscience.  So experiments have to be very carefully designed if they are to eliminate the effects of predisposing factors such as priming in decision-making, such that decisions are not influenced by uncontrolled unconscious factors (hence truly "free will").  However, if "free will" doesn't exist, then eliminating all predisposing factors will ultimately prove futile, so until researchers can control for all variables, some doubt will always remain.

Nonetheless, research in this field has significantly changed our understanding of the role of "thought" or "will" or "volition" in the causal chain, such that they now appear to be a side-effect rather than cause of physical action.


What is the psychology behind the need to be the centre of attention?

Depends on the pattern of how this occurs -- the situation, consistency, and severity.

If across situations, across different other people, and across different settings, this would indicate a personality trait. The person might be unaware of the social cues of others and draw attention to ideas that are interesting to them. Most people are interested in talking about themselves. Combine this tendency with lack of awareness, and you might see what you're describing.

If they consistently dominate the group conversation across different people and different situations, to the point where the pattern negatively affects their life or work, they might have a narcissistic trait or even NPD. In such case, the person's concept of self-worth may be abnormally modulated by the positive attention they receive from others. They might have a need to be the focus of attention, because otherwise they may feel degrees of worthlessness. This need may have developed during childhood from one or a series of traumatic events (i.e. narcissistic parent).

If this happens consistently only with one group of people, it could be that the people in the group consistently have conversations that are uninteresting to the person.

Additionally, the group of people might be meeting in a certain place or a certain time, during which the person might be more likely to want to talk about themselves. Perhaps, the group meets after the person has finished their soccer practice, or after a weekly meeting with their boss. If so, the person might be particularly excited to talk about their game events, or how pressured they feel at work.


How can I find open access journals for cognitive science research?

The Directory of Open Access Journals is a great place to start when searching for Open Access Journals in any field.

You can browse through journals for the specific subject areas like Psychology or Neurology, or you can search for journals or articles containing certain keywords.

The DOAJ lists articles in multiple languages as well, not just English journals.


How to compare linear and categorical models of perceptual comparisons?

This sounds a lot like tests of categorical perception done in psycholinguistics. Categorical perception states that people perceive phonemes categorically, even though the acoustic signal varies continuously.
For example, the phonemes $/b/$ and $/p/$ differ on only one acoustic feature: voice onset time. Using computer synthesized speech, one can experimentally manipulate the voice onset time along a continuous dimension. In a prototypical experiment, subjects are asked to identify each sound as a $/b/$ or $/p/$. If perception were continuous, you might expect that the proportion of $/b/$ responses varies linearly with the voice onset time-- but it doesn't. As you can see in the red line, there is a sharp drop around 20ms in which people perceive everything to the left as $/b/$ and everything to the right as $/p/$.

Another way to see this is to plot discriminability (blue line). Here, participants are presented two stimuli from adjacent VOT bins and asked to judge which one matches a 'target' stimulus. Generally, people perform near chance at discriminating between the two phonemes unless the two stimuli cross the VOT boundary. Again, if perception were linear, you might expect a straight blue line rather than a peaked one.
Most researchers will use t-tests or ANOVA to test for differences of between and within category discrimination. For instance, one might conduct a series of t-tests on discriminability to show that only when stimuli cross the VOT boundary can subjects reliably discriminate them.
For an example of these tests in practice, see Morford et al. (2008). Note that some researchers have found conflicting results when using different dependent measures. For example, Massaro & Cohen (1983) asked participants to make continuous judgments of stimuli and found no evidence of categorical perception.
Another alternative might be to find the best fitting line and the best fitting sigmoid curve, and compute the Bayesian Information Criterion for each. The one with the lower BIC is the preferred model. For regression analysis, BIC can be calculated as

$BIC = n\log(\frac{RSS}{n}) + p\log(n)$

where n is the number of data points in the model, p is the number of free parameters, and RSS is the residual sum of squares.
The drawback of using BIC is that it only tells you something about comparative model fit. If both linear and sigmoidal models were a bad fit for the data, BIC would not tell you that.

Massaro, D. W., & Cohen, M. M. (1983). Categorical or continuous speech perception: A new test. Speech Communication, 2(1), 15-35. PDF
Morford, J. P., Grieve-Smith, A. B., MacFarlane, J., Staley, J., & Waters, G. (2008). Effects of language experience on the perception of American Sign Language. Cognition, 109(1), 41-53. PDF


Does a non-knowledge based, or knowledge corrected IQ test exist, and what are its results per race?

No, such a completely knowledge-free test has not been devised. Fluid intelligence (a component of IQ tests) is probably the closest thing to the claim of being "knowledge-free", but it isn't quite so. As typically measured, e.g. using Raven's progressive matrices one still needs to have some clue what the test is talking about in terms patterns etc. And prior exposure to similar test makes a difference (see Hayes et al. 2015) in test results, i.e. there's a learning effect.

In the US, where most such race-intelligence research is conducted, there's still a racial group difference on fluid intelligence tests (e.g. Raven's) in the usual test settings, although some evidence suggests it depends how the test is interpreted by the takers may matter, e.g. Brown & Day (2006):

  This study addresses recent criticisms aimed at the interpretation of stereotype threat research and methodological weaknesses of previous studies that have examined race differences on Raven's Advanced Progressive Matrices (APM). African American and White undergraduates completed the APM under three conditions. In two threat conditions, participants received either standard APM instructions (standard threat) or were told that the APM was an IQ test (high threat). In a low threat condition, participants were told that the APM was a set of puzzles and that the researchers wanted their opinions of them. Results supported the stereotype threat interpretation of race differences in cognitive ability test scores. Although African American participants underperformed Whites under both standard and high threat instructions, they performed just as well as Whites did under low threat instructions.

A slightly more recent meta-analysis (Nguyen & Ryan 2008) still found an effect though

  For minorities, moderately explicit stereotype threat-activating cues produced the largest effect, followed by blatant and subtle cues: ds = |.64|, |.41|, and |.22|, respectively; explicit removal strategies enhanced stereotype threat effects compared with subtle strategies: ds = |.80| and |.34|, respectively.

Alas most such meta-analytic research does not isolate just one type of IQ testing.

IQ testing under stereotype threats is still a pretty controversial area of research in itself, see Ziegler (2017) and reply by Nguyen & Ryan.


A definition of hatred towards your own nation

The word "Oikophobia" has several different definitions.  In psychology, it usually means an aversion to home surroundings, or to objects in the home.  However, the British philosopher Roger Scruton coined a new meaning, which is exactly what you are looking for:

  The disposition, in any conflict, to side with 'them' against 'us', and the felt need to denigrate the customs, culture and institutions that are identifiably 'ours'.
  -  Roger Scruton, quoted on Urban Dictionary

Wikipedia has a more detailed description of the term:

  Scruton uses the term as the antithesis of xenophobia. In his book, Roger Scruton: Philosopher on Dover Beach, Mark Dooley describes oikophobia as centered within the Western academic establishment on "both the common culture of the West, and the old educational curriculum that sought to transmit its humane values." This disposition has grown out of, for example, the writings of Jacques Derrida and of Michel Foucault's "assault on 'bourgeois' society result[ing] in an 'anti-culture' that took direct aim at holy and sacred things, condemning and repudiating them as oppressive and power-ridden."

  "Derrida is a classic oikophobe in so far as he repudiates the longing for home that the Western theological, legal, and literary traditions satisfy. . . . Derrida's deconstruction seeks to block the path to this 'core experience' of membership, preferring instead a rootless existence founded 'upon nothing.'"

  An extreme aversion to the sacred and the thwarting of the connection of the sacred to the culture of the West is described as the underlying motif of oikophobia; and not the substitution of Judeo-Christianity by another coherent system of belief. The paradox of the oikophobe seems to be that any opposition directed at the theological and cultural tradition of the West is to be encouraged even if it is "significantly more parochial, exclusivist, patriarchal, and ethnocentric."  Scruton described "a chronic form of oikophobia [which] has spread through the American universities, in the guise of political correctness."

  Scruton's usage has been taken up by some American political commentators to refer to what they see as a rejection of traditional American culture by the liberal elite. In August 2010 James Taranto wrote a column in the Wall Street Journal entitled Oikophobia, Why the liberal elite finds Americans revolting in which he criticized supporters of the proposed Islamic center in New York as oikophobes who were defending Muslims who aimed to "exploit the 9/11 atrocity".
  -  Wikipedia


mirror-writing using non-dominant hand easier with closed eyes

There has been some recorded research in this area from more than 150 years back (1858). The concept is called Bilateral transfer of learning.

Definition:
"Bilateral transfer is an aspect of the transfer of learning and is the transfer of learning or performance from one side of the body after training to the other. So, for example, after training a task with the right hand there, is an improvement in left handed performance."

I could also find a mention of this very specific example (Ref: Slide #8 in this slideshare presentation)-

"He (E H Weber) observed that some children trained to write with the right hand were able without further training to produce very good mirror writing with the left hand".

Why closing the eyes helps may be due to the fact that it reduces distraction but I haven't been able to find any reference for this.


From a psychosocial standpoint, how is violence different from aggression?

The definition of aggression and violence is a thorny issue, and there is considerable disagreement about the terms between disciplines, but also within disciplines. Sometimes authors use the terms interchangeably.

In psychology, the term aggression is often used as the broader term that encompasses all forms of harmful behavior.

For example, according to the widely cited definition by Baron and Richardson (1994), "aggression is any form of behavior directed toward the goal of harming or injuring another living being who is motivated to avoid such treatment". This would include verbal aggression, or indirect forms of aggression such as gossiping.

In contrast, the term violence is often limited to extreme forms of physical aggression.

For example, Anderson (2000) defines violence in the Encyclopedia of Psychology as

  a subtype of aggression, generally used to denote extreme forms of aggression such as murder, rape, and assault. All violence is aggression, but many forms of aggression are not violent.

References

Baron, R. A., & Richardson, D. (1994). Human aggression. New York: Plenum Press.

Anderson (2000). Aggression and violence. In A.E. Kazdin (Ed.) Encyclopedia of psychology, 8, 162-169. New York & Washington D.C.: Oxford University Press and the American Psychological Association.


Do humans really feel that a \$99 price tag is significantly lower than a \$100 one?

The Wikipedia page of Psychological Pricing giving this chart:

Why?

  Kaushik Basu used game theory in 1997 to argue that rational consumers value their own time and effort at calculation. Such consumers process the price from left to right and tend to mentally replace the last two digits of the price with an estimate of the mean "cent component" of all goods in the marketplace.

Also related on UX Stack Exchange: Is there any advantage in marketing my product for £99.99 instead of £100?


What can one do to permanently increase one's baseline happiness (subjective well-being)?

Going off the findings in this paper, it seems that one's baseline level of happiness can be increased and maintained at a (weakly) significant level by "continual effort and engagement in  some  intentional  process" (Sheldon & Lyubomirsky, 2006, pg. 59), which the authors refer to as "activity-based changes". Examples given include, starting to exercise, beginning a new project, or gaining a new perspective.
This as opposed to circumstance-based changes which deliver only minimal, short-lived increases in happiness, such as getting a raise, or buying a new car.
I feel it is important to note that this is only one paper which uses a short time frame of only 6 months to measures changes in happiness. However, it seems then that to achieve lasting increases in our happiness set point, we are better off working on ourselves than our surroundings.


How to estimate an expected effect size for a planned psychology study?

The purpose of reviewing the literature for effect sizes is to form an estimate of what effect size you might expect in your present study.

Existing meta-analysis: The principles and techniques of meta-analysis provide a good starting point for generating a predicted effect size.
If a meta-analysis has already been conducted, then the estimated population mean and confidence intervals of effect sizes is a useful piece of information.
In some cases there will also be a moderator analysis reported which tests whether the effect size varies as a function of the moderator (e.g., adults versus children; lab versus field, etc.). If your study matches one level of an influential moderator, then it may be worth weighting estimates more by the estimated effect size for that moderator.

No existing meta-analysis: If no meta-analysis exists or if one exists but is out of date, then you may want to perform your own meta-analysis. There are several great books on meta-analysis. I've personally found Borenstein et al (2011) to be a good introduction and Hunter and Schmidt (2004) to be useful  particularly if you are interested in correlations and various corrections. Here is a link to an overview of meta-analysis.
Conducting a rigorous meta-analysis for publication is a technical and resource intensive process. However, if all you want is a ball-park estimate of expected effect size for sample size and study design considerations (i.e., your not doing an explicit meta-analysis publication), then it may be more pragmatic to just do a quick informal meta-analysis.  In some cases there might only be one or a few studies which are similar to your study. In this case, the meta-analysis can be very simple.

Generalisation: Another issue that comes up is generalisation. Students sometimes say to me that there have been no other studies like the one being conducted. This may be true, but at some level of generality this is almost always false. If a study is about a particular training program in the work place, then a meta-analysis of training in general may be informative. If the intervention has only been used with teenagers and is now being applied to adults, the meta-analysis of teenagers would be relevant. Broadly, theory should be applied to assess the likely generality of any broader research to the present study.

Theory: Theory is important in many respects. Theory may suggest that a particular modification to the design should increase or decrease the effect size relative to a previous studies.

Aggregating estimates: In general it is is important to consider how different effect size estimates should be aggregated. The more similar a previous study is to the present study, the more weight should be given to any effect size estimate. In this case, similarity requires theoretical judgement about what are the important factors that might moderate the effect. Similarly any aggregation needs to be mindful of sample size considerations where larger sample sizes will increase the precision of the estimate in any given study. Thus, at the ultra-specific, the present study may be an exact replication of a previous study. At another level, there may be meta-analytic evidence from similar studies. At an even broader level Jacob Cohen reluctantly proposed various rough rules of thumb of what to expect for small, medium, and large effects in behavioural science studies.

Importance of uncertainty: Another point is that you don't actually know the population effect size for your study. That's why you are doing the study. There will always be uncertainty about your effect size estimate. It can even be useful to quantify that uncertainty either using meta-analytic confidence intervals or something more ad hoc.
This is analogous to the concept of a subjective bayesian prior probability on a parameter of interest. See for example, this discussion of eliciting priors from experts. Meta-analysis provides some methods for quantifying uncertainty in an effect size estimate, but this may not be entirely appropriate given that you are not trying to generalise to the variation in the whole world of effect sizes. Rather you are trying to generalise a prediction for a specific study, and you may be pooling many different pieces of information, some quantitative, and some qualitative.

By way of example, I do research on personality faking. I am aware of a meta-analysis of the mean effect size of faking versus honest personality responses (e.g., perhaps around d = .6). However, I also know from previous research that the type of faking instructions makes a big difference to the expected effect size (e.g., if you tell people to fake you often get approximate d = 1.0 and if you just put people in a context with a motivation to fake you get approximate d = .3). Thus, If I were calculating expected effect size for any given study I would combine knowledge of the nature of my faking instructions with various meta-analytic estimates. I'd weight my own previous studies highly because they typically share more similar features (e.g., same personality test, similar participants, etc.) than the general literature. I'd also acknowledge the uncertainty in my estimate.

References

Borenstein, M., Hedges, L. V., Higgins, J. P., & Rothstein, H. R. (2011). Introduction to meta-analysis. Wiley.
Hunter, J. E., & Schmidt, F. L. (2004). Methods of meta-analysis: Correcting error and bias in research findings. SAGE Publications, Incorporated.


Prevalence of mental health problems in medical professionals caused by exposure to death?

I believe, and I do not know if good quality epidemiological evidence exists, that such situations may trigger abnormal illness representations among medical professionals. Factitious disorders, for instance, I believe could be some way to deflect depression in some individuals. Along with abnormal illness representations could also come abnormal moral representations of illness, which, if not outright religious, links in somewhat with the notion of salvation.

Studies concerning abnormal illness representations are usually concerned with patient's illness representations. I see no epidemiological studies or data concerning the illness representations of medical staff, would be medical staff, or former medical staff (for instance, those who quit after traumatic experiences with patients) when they present as patients. Indeed, calling into question the illness representations of medical staff is not exactly politically correct. It's even a rather effective way to get you labelled as psychotic in some flavour or another.

However, from a clinical perspective, (i.e. with a clinical bias) a risk factor for factitious disorder is when someone has or has had a professional wish of working in the health care field. Such as a medical doctor who went into depression after a patient died and who did not fully get over it...

I'd love to know what data there really is out there to back up this clinical claim. Best I could find is Lois Krahn's work at Mayo Clinic:

https://www.ncbi.nlm.nih.gov/pubmed/12777276

To me, this is an extreme manifestation of more common mental issues affecting medical professionals.


What cognitive bias prevents you from discarding stuff?

One possible explanation for the scenario you are describing is Endowment effect.

  In psychology and behavioral economics, the endowment effect is the
  hypothesis that people ascribe more value to things merely because
  they own them.

One of the theories that explain the phenomenon is based on loss
aversion :

  It was proposed by Kahneman and his colleagues that the
  endowment effect is, in part, due to the fact that once a person owns
  an item, forgoing it feels like a loss, and humans are loss-averse.


What is the difference between solving a problem and acquiring a skill?

To take your concrete examples, there are several broad distinctions relevant to comparing a task like chess and a task like playing Pac Man.
Cognitive versus psychomotor skill

Research on learning and task performance is divided into various domains of tasks. Two such domains are cognitive, of which chess would be an example, and psychomotor, of which Pac Man would be an example. Video games vary in the relative importance of cognitive versus psychomotor skill.

You might want to read the Annual Review of Psychology article by Rosenbaum, and Carlson, and Gilmore, 2001, PDF "Acquisition of intellectual and perceptual-motor skills". The article provides an overview of the similarities and differences between cognitive and psychomotor skill acquisition.

Traditionally, the word "skill" has had psychomotor connotations. But ultimately the defining feature of a skill is that it is acquired through practice, and this applies well to cognitive as it does to psychomotor tasks.

Learning versus performance

Some research focuses on how learning occurs, whether it be studying the relationship between practice and performance, examining changes in the errors made over time, and so forth (e.g., see this review by Heathcote et al PDF, called "The power law repealed: The case for an exponential law of practice" which is on the mathematical functional form of the learning curve).
Other research focuses on performance itself. What are the cognitive processes that underlie performance? In such studies, learning is often a nuisance factor.
Thus, in the case of both Chess or Pac Man you could focus on either the process of learning or on performance itself (whether it be of a novice or expert).

Task complexity and time frames of learning

Research in skill acquisition can broadly be distinguished in terms of the typical time frame it takes to acquire the skill of interest.
Typical skill acquisition research that is done in the lab involves tasks where meaningful learning can be observed in hours or perhaps days.
Some other skills can take years to acquire, and this is broadly studied in what is sometimes referred to as the "expertise literature". There have been many studies of chess within the expertise literature. See for example this paper on "the role of deliberate practice in  chess expertise" PDF by Charness, Tuffiash, Krampe, Reingold, & Vasyukova, (2005).
With regards to this distinction, Pac Man presents some difficulty. No doubt one could study meaningful learning in the short term, but also that it might be possible to focus on the learning that might occur for a true Pac Man master who had devoted years to perfecting the art of escaping ghosts and eating little pellets.


Have there been followups to the Rosenhan Experiment?

There was a follow-up to Rosenhan (1973).  The whole study was revisited by Scribner (2001).

  The present study is a replication of sorts, modified to suit the contemporary, postdeinstitutionalization state of mental health care. The findings suggest that a significant shift has occurred in mental health care since 1973. At the time of the original study by Rosenhan (1973), the troubling issue was the ease with which people could receive an unwarranted diagnosis and unnecessary treatment for a nonexistent mental disorder. In today's mental health care environment, the troubling issue is the difficulty involved in obtaining treatment that is warranted for conditions that are present.

References

Rosenhan, D. L. (1973). On being sane in insane places. Science, 179(4070), 250-258. DOI: 10.1126/science.179.4070.250

Scribner, C. M. (2001). Rosenhan revisited. Professional Psychology: Research and Practice, 32(2), 215. DOI: 10.1037/0735-7028.32.2.215


The interactions between hallucinations and reality in people with schizophrenia

Unfortunately hallucinations of visual type seldom occur with schizophrenia. When visual hallucinations occur in schizophrenia or more frequently (but still uncommon) in other disorders they are rather unlike a simulation of the current world - e.g. a closed door becoming open in the room. In addition patient in a hallucinatory state is very affectively taken by the experience and often is just afraid to move. Further - the only way to know would be to ask the patient as to what happened, but given that this kind of event is very rarely, if at all, happening, there is no answer because - how can you set up an experiment. Therefore this question, interesting though it may be, is just of speculative value.

A good article about the topic is:

M Manford  F Andermann, Complex visual hallucinations. Clinical and neurobiological insights. Brain, Volume 121, Issue 10, 1 October 1998, Pages 1819–1840


Why do some people react verbally to intrusive thoughts and/or embarrassing memories?

It might be a way of distracting ourselves, to change the subject and deviate the focus from thoughts we don't like to anything our mind makes up.

  When anxiety becomes overwhelming, it is the ego's place to protect the person by employing defence mechanisms. Guilt, embarrassment and shame often accompany anxiety.
  https://en.wikipedia.org/wiki/Defence_mechanisms

It is also possible that some of us use this as a way to acknowledge their feelings of shame. we can see this when laughing (when its a honest laughter), as it effectively relax the athmosphere.

But in any case, we can't "get rid" of a thought. It is only discarded from the present moment and may be intrusive again at another inopportune moment; until we address the issue.


Freud's theory regarding child to parent attraction

Both are true, to my knowledge (in the sense that Freud did believe this). They relate to the Oedipus and Electra complexes, which are are core parts of classical Freudian theory.

Children, through the Oedipus and Electra complexes during the phallic developmental stage, where they sexually desire their same-sex parent, eventually come to identify with their same-sex parent by resolving these desires through different mechanisms. These mechanisms are castration anxiety, in boys, and penis envy, in girls.

He believed that these mechanisms would lead to partner preferences matching the same-sex parent. Freud also believed that failing to successfully resolve the Oedipus or Electra complex could lead to a host of "problems" in adulthood, like neurosis, pedophilia and homosexuality.

I don't need to say that this classical view is outdated and not supported by evidence or modern theories.


How cognitive science explain the stylistic convention in text writing?

I don't think there is a stylistic convention in text writing that prevent the expression of an opinion. There are countless texts expressing a subjective view or controversial points. The example you picked up is somehow very specific to academia.stackexchange.com.

The website explicitly tries to prevent the expression of an opinion - see https://academia.stackexchange.com/help/dont-ask about the possible reasons for a question to be flagged (and removed) as primarily opinion-based - e.g. a rant in disguise. This rule echoes the way science is made of - facts and interpretation -, especially in its formal way of communication. Researchers sometimes express an opinion in an article but it is usually advertised as such - see the specific section called "opinions" in the journal Trends in Cognitive Science for example.

In the case of the removed sentence, I guess that the reviewer relied on "I would prefer" and "my opinion" to build his/her opinion.


Funnily enough, there was a Science article published on this (see here).

In their sample of university students, Mehl et al. had participants wear a specialized device that recorded audio samples from daily life (The EAR). They report that (emphasis mine):

  The data suggest that women spoke on average 16,215 (SD = 7301) words and men 15,669 (SD = 8633) words over an assumed period of, on average, 17 waking hours. Expressed in a common effect-size metric (Cohen’s d = 0.07), this sex difference in daily word use (546 words) is equal to only 7% of the standardized variability among women and men. Further, the difference does not meet conventional thresholds for statistical significance (P = 0.248, one-sided test). Thus, the data fail to reveal a reliable sex difference in daily word use. Women and men both use on average about 16,000 words per day, with very large individual differences around this mean.

Although, it's possible that we might see systematic differences depending on factors other than sex (e.g., SES, age).

References

Mehl, M. R., Vazire, S., Ramírez-Esparza, N., Slatcher, R. B., & Pennebaker, J. W. (2007). Are women really more talkative than men?. Science, 317(5834), 82-82.


I recommend looking at the literature on aggressive behavior, e.g., https://en.wikipedia.org/wiki/Aggression. There are many potential causes for such an act. In terms of generic predispositions, consider personality types (e.g., low Agreeableness), but don't overlook the importance of context and culture (e.g., high wealth inequality).

As to the final question, self-help questions are out of scope for this forum.


If you look at the phenomenon of lucid dreaming, where people consciously explore their dreams, you will recognize that perfect virtual reality is possible with the biology that is already in place.

The lucid dreaming related phenomenon called "false awakening" is another piece of evidence for perfect virtual reality. When a lucid dreamer experiences a false awakening, it is indistinguishable from reality. A person  wakes up in the same bed. walks through replica rooms. Such person may use restroom, brush teeth, start making breakfast, then wake up in reality. The only two consistent differences between a false awakening and reality would be inability to see consistent time on a digital display and inability to adjust light levels with light switches. The defining characteristic of false awakenings is that they trick the dreamer into thinking the dreamer is interacting with reality.

I should probably mention that expert dreamers, those who keep a dream journal and train to remember dreams, experience their dreams more intensely. As such, it is not uncommon to hear of "hyper-real" dreams, which are more visually and cognitively clear than baseline reality.


Hutchinson, B. (2002), an article in the book Synergy Matters by Adrian M. Castell may help in understanding what is meant by bottom up thinking and the opposite, top down thinking.

[T]he  term  ‘top  down’  is  used to  describe an  approach  to  problem solving  where  the  problem  space  is  defined  first.  The  worldviews  of  the  participants are used  to  conceptualise  the  desired  state  of  the  proposed system.  Once  this  is achieved,  the  system  is  developed  within  this  boundary.  The  components,  or subsystems  are  derived  within  the  context  of  the  predefined  desired state. The  term  ‘bottom  up’  is  used  to  describe  an  approach  where  no  assumptions  are  made about the  boundary  of  the  problem  space.  The  behaviour  of  component  parts  are rationally  observed  to  determine  the  properties they  have.  Management  decisions, or system designs  are  then  based  on  the  observed  behaviour  of  components.

An example given in the conclusions is:

[I]nvestigating a system failure in bottom up mode would look for causes at the element level, or more precisely, at their interactions. The top down mode would tend to look at the overall system, and would put ‘blame’ on the system itself and how it functions, rather than emergent properties of system element interactions.

Think of it like a brick building.  You need to build it from the bottom up, with each brick being correctly placed to form the correct shape etc.  If the bricks are placed differently, you may get a different building, or maybe you will get the same building but badly constructed.
Take the following as a more detailed example comparison...
There is a team of researchers working on a task and each member inputs their findings into a computer system which analyses the results and comes up with a conclusion.
The program relies on accurate information from each team member entry but there was a slight error in a couple of entries producing an incorrect conclusion by the system.
A top down thinker would blame the computer system analysing the results.  A bottom up thinker would analyse what the system was analysing and how, leading to them finding the real cause.
References
Hutchinson, B. (2002). Bottom up thinking. In Synergy Matters (pp. 445-450). Springer, Boston, MA. doi: 10.1007/0-306-47467-0_75Preview available in Google Books


Is it true that mirror neurons can make a man with an amputated arm feel sensation just by looking at someone else's arm, like Ramachandran said?

Mirror neurons exist and have been recorded from in primates and humans - these are cells that respond to the actions and inferred perceptions of others.
In papers by Ramachandran and others, they have shown that patients who have their arm anesthetized report experiencing a sensation of touch when they see someone else's arm touched:
Case, L. K., Abrams, R. A., & Ramachandran, V. S. (2010). Immediate interpersonal and intermanual referral of sensations following anesthetic block of one arm. Archives of neurology, 67(12), 1521-1523.
Case, L. K., Gosavi, R., & Ramachandran, V. S. (2013). Heightened motor and sensory (mirror-touch) referral induced by nerve block or topical anesthetic. Neuropsychologia, 51(10), 1823-1828.
These papers of course strongly suggest, but do not necessarily prove, that these phenomena occur due to mirror neurons.


How many times on average do people wake up per night?

Based on this paragraph from the Wikipedia article on hypnograms

On a hypnogram, a sleep cycle is usually around 90 minutes and there are four to six cycles of REM/NREM stages that occur during a major period of sleep.
Most SWS occurs in the first one or two cycles; this is the deepest period of sleep. The second half of the sleeping period contains most REM sleep and little or no SWS and may contain brief periods of wakefulness which can be recorded but are not usually perceived.
The stage that occurs before waking is normally REM sleep.

And this image (also from wiki):
Sample hypnogram showing one sleep cycle (the first of the night) from NREM through REM
A normal and healthy person usually wakes for a brief time after his/her REM stage was finished in each sleep cycle. So, if we consider A 7–8-hour sleep probably includes four cycles, and each cycle include at least one REM, then each person at least wake four times.


Are we biased against other people's suggestions?

It can be caused by reactance - automatic opposite response preventing actions that threatens behavioral freedom. You can find more about reactance in:
Baron, Robert A.; et al. (2006). Social Psychology. Pearson. ISBN 9780205444120.
Roeckelein, J. E., ed. (2006). "Reactance theory". Elsevier's Dictionary of Psychological Theories. Elsevier. pp. 507–508. ISBN 9780080460642.


Are animal instincts and preferences based on some brain micro structures?

There is the structure called the Fusiform-face area (FFA), which is located in the low tempero-parietal region. In human studies, the FFA has shown to highlight strongly when you look at a human face, as opposed to any other (inanimate) object. This is what the region got its name from.

However, it is believed that the FFA is not necessarily a face area (See "Function and Controversy" on the Wiki page). Instead, researchers argue that the area is a visual expertise area. Where we, as humans, are experts in recognizing faces, zebras, for instance, are incredibly good at distinguishing the stripes of other zebras.

This even goes for within-species differences. Western people that have never worked with Chinese symbols will show little to no activation in the FFA, whereas Chinese people that use it daily will show this activation. This would also explain cross-race recognition (thanks Josh) i.e. it is easier to distinguish people from the same race then someone from different races.

With regard to your question about preferences: I don't know for sure. I have heard that people like what they know. That would imply that whatever the FFA is expert in, is more preferable to the person/animal. I have no reference, so if anyone does have some, I welcome you to edit my answer or post your own.


Is this expected to happen while asleep?

The appropriate answer is that dreams are generally not in any way diagnostic of a health issue. Being able to read while dreaming is absolutely not diagnostic. I can't imagine that any reputable research has been done on this topic.


Does James Holmes diagnosis of schizotypal personality disorder indicate a predisposition for mass murder?

So the question is

does schizotypal personality disorder explain lifelong homicidal ideation / obsession, or predisposition to same?

Schizotypal personality disorder does include paranoid ideation among its symptoms. Paranoid ideation has been linked to homicidal behavior in some studies

Patients who reported homicide attempts could be distinguished from patients with no homicidal behaviors by the presence of other aggressive behavior such as suicidal ideation and suicide attempts by themselves and their family members and by elevated current measures of interpersonal sensitivity, hostility, and paranoid ideation.

As to whether it's enough to "explain" such behavior... that's a tricky question as it depends on what you mean by "explain". If you interpret "explain" as "makes it more likely", a psychiatrists would say yes. If you interpret "explain" as "excuses in the eyes of the law", a jurist would say no.
According to Wikipedia (which does not cite any ref for this)

Most courts accept a major mental illness such as psychosis but will not accept the diagnosis of a personality disorder for the purposes of an insanity defense

Note however that the distinction between personality disorders and the rest (formerly axis I) has been abolished in DSM 5. So this is an area of fairly recent changes in psychiatric thinking. I don't know how courts will react (or maybe some have done so already) in reaction to this change in the DSM. N.B. you'll probably want to read https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811091/ for more on the criminal law and personality disorders; it's written in 2013 (so after the adoption of DSM-5), but doesn't mention any cases where the new categorizatoin has influenced criminal-law decisions. I guess it was still too early for that. See also http://jaapl.org/content/42/2/141.long which is more focused on the DSM-5 change. From the latter is worth quoting:

The DSM-5 contains an expanded Cautionary Statement of explicit relevance to forensic psychiatry. It states in part that, “In most situations, the clinical diagnosis of a DSM-5 mental disorder … does not imply that an individual meets legal criteria for the presence of a mental disorder or a specified legal standard… .” It goes on to state that, “a diagnosis does not carry any necessary implications regarding the … individual's degree of control over behaviors that may be associated with the disorder” (Ref. 3, p 25).

So again a psychiatrist's view and a the law's view are different. Note than in mostly non-US (but still English-law-based) jurisdictions, there's a notion of diminished responsibility, often applied in cases of mental illness contributing to a crime. The US law use of this notion of diminished responsibility appears very limited; it seems to be used mostly in California (but not in Colorado where Holmes was tried.)
And since we're talking serial killers with psychotic tendencies it's probably worth recalling the case of Breivik and Norwegian law. It's hard to summarize that case here since it's an entire saga with front-page disagreements on the diagnosis etc., as well as peculiarities of the Norwegian law with respect to mental illness definitions. But in the case of Breivik, just like in that of Holmes, there was no agreement among psychiatrist what his diagnosis should be. In Breivik's case the court ultimately accepted the personality disorder diagnosis rather than an axis I diagnosis proposed by some psychiatrists. In the case of Holmes the alternative diagnosis was schizoaffective disorder, offered by another court-appointed psychiatrist. Given the difference in law between Colorado and Norway, it's less relevant what Holmes' actual diagnosis was; in Norway a psychotic disorder automatically qualified as incompetence to stand trial, but not in Colorado, where the M'Naghten test (telling right from wrong) applies.
And coming back to the meaning of "explain", the latter psychiatrist who examined Holmes said:

Metzner, who diagnosed Holmes with schizoaffective disorder, said he did not think Holmes went on his rampage to get notoriety or because of his longstanding hatred of mankind, which he described in a spiral notebook. Instead, Metzner said, Holmes' actions were "directly related" to delusions that killing people would increase his self-worth.
"I can come up with no other explanation for what he did," Metzner said.
Holmes knew what he was doing was illegal and that others would think it was wrong, Metzner reiterated in response to questions from District Attorney George Brauchler. The prosecutor brought up Holmes' statement that he did not want to date someone because he did not want anyone to be featured in news coverage as the girlfriend of a mass killer.

And paralleling the Berivik case, the judge didn't dig this

[Judge] Samour ordered a second evaluation after he found Metzner’s report was “incomplete and inadequate.”

And regarding some of the subsequent questions

Is it likely that such ideation could be kept secret for one's whole life?

Schizotypal personality disorder also has among symptoms a "reduced capacity for close relationships" usually manifested as "lack of close friends". So that makes it more likely such individuals will not have many people they could talk to about their weird ideas, so they may not get noticed until it's too late.
From the unsealed notes of Dr. Fenton and Ms. Roath

Holmes had been referred to Dr Fenton by University of Colorado social worker Margaret Roath in March 2012, who noted it was “hard to interview him as he would just start and take a long time to answer”.
“When I asked him about other symptoms, he said he did not want to say as I would have to report him. He says he wants to kill other people, but no one in particular and has never done anything to harm others,” Roath noted.
A note of Obsessive-Compulsive Disorder was accompanied by the description that “(Holmes) has problems concentrating, eats OK, does not have crying spells and does not have thoughts of suicide.”
In an email to Dr Fenton to see him “soon if possible”, Ms Roath described Holmes was the “most anxious guy I have seen”.
“Most concerning is that he has thoughts of killing others people, though I do not think he is dangerous,” she said, adding Dr Fenton would see him as it “might be best to keep him in the system”. [...]
In her notes, Dr Fenton expressed concern over Holmes’s homicidal thoughts but his lack of a willingness to address specifics with her. He told her if she revealed more details she would “lock him up.”
Those in charge of his courses has told her of his “extremely awkward” social interactions and “odd comments”, but “neither had heard of him making threatening remarks”, she noted in a June client summary.
A background check had revealed no weapons permits, she said.
“At this point. James is … intermittently functioning at a psychotic level,” Dr Fenton wrote.
But she concluded he “does not currently meet criteria for a mental health hold”.
“He is not gravely disabled and has no evidence of suicidal ideation. Longstanding homicidal ideation but denies any specific targets and there is no current evidence he is angry at the grad school (or anyone else).”
She noted that while Holmes had made hostile remarks to her and another psychiatrist, he had not made threats.

Captioned: "Psychiatric notes released to public. This one, a mental status exam, by Dr Fenton"

So your (2nd) question becomes mostly hypothetical in view of this. Also, whatever obscure statement he may have made to a friend about "floodgates" pale in comparison to the more direct statements made to mental health professionals before the murders, although had a professional heard those, they might have seen it as a sign he was going to act. We can only speculate at this point what some professional might have done corroborating all the evidence.
As an aside, Fenton was sued in 2013 by some victims' relatives. Fenton did warn someone on the campus police:

The documents show Fenton went to University of Colorado police officer Lynn Whitten and informed her that Holmes confessed homicidal thoughts to her and that he was a danger to the public, "per her requirement," the documents say. Whitten responded "by deactivating Holmes' key-card access to secure areas of University of Colorado medical campus buildings," the Denver Post writes. Fenton also told Whitten that Holmes had "stopped seeing her and had begun threatening her via text message," the documents state.

There's a bit more of the campus-level story:

Holmes started seeing Fenton in 2012 to help with his social anxiety. He soon confided that he was having thoughts about killing people.
His last visit was June 11, 2012. By then he had already amassed an arsenal of weapons and body armor and was meticulously planning his attack on a packed showing of a new Batman movie. But all Holmes told Fenton and another psychiatrist, Robert Feinstein, was that he had failed a key exam and was dropping out of the neuroscience program.
Holmes "left in a huff," Fenton told Whitten, whom she called the same day. She was concerned because Homes had told her "I want to kill as many people as possible," and she wondered if he was nearing a psychotic break, according to the documents.
Though he had "constant homicidal thoughts," Fenton told Whitten, he had never revealed specific targets or plans. But Whitten wrote in her notes that "Holmes indicated to Fenton that he liked thinking about it."
Fenton was alarmed enough to violate Holmes' health privacy rights and call his mother, Arlene. But Fenton did not tell Arlene Holmes about her son's homicidal obsession, instead mentioning that he'd dropped out of school.
The documents show that Fenton found Holmes' mother's reaction reassuring.
She left a voicemail for Whitten: "It's pretty good news on our guy James. It sounds like he's always been like this. I've talked to his mom, she and the dad are kind of putting some quiet support in place. They've got my number in case they need anything."
She concluded: "So, anyway, I think we've got everything in place for now, so if something else comes up I'll let you know."
Arlene Holmes testified during the trial that Fenton didn't return her calls seeking more information. Fenton chose not to detain Holmes because she felt he was "on the borderline" and didn't think it would help, she told Whitten, according to the documents provided by the university.
About the same time, Fenton called University of Colorado professor Sukumar Vijayaraghavan, head of the neuroscience program, about Holmes, according to documents provided by prosecutors.
"James had told her (Fenton) he did not think he would make a mark on the world with science so he could blow up people and become famous," Vijayaraghavan told Aurora police after the shooting. Vijayaraghavan said he then called Whitten, who told him "action would be taken immediately." She said she had suspended his student ID and "police are aware of the situation and are keeping an eye on the whole thing."
After the shooting, Whitten told Aurora police she "discussed Holmes" with her sergeant and checked with others on the status of his withdrawal from the university.
[...]
The university said in a statement that its faculty and staff acted responsibly. Campus police officer Lynn Whitten, who was not named in the lawsuit, has since retired. Her attorney, Tom Rice, said she did all that she could with the limited information she had, none of which gave her reason to believe Holmes was an imminent danger.

From this one can guess that the civl lawsuit against Fenton didn't get far because:

Under Colorado law, mental health professionals cannot be held liable in civil suits for failing to predict a patient’s violent actions unless it involves a “serious threat of imminent physical violence against a specific person or persons.”

And I was right on the money, the lawsuit against Fenton was dismissed in 2016.


The answer ought to be a qualified "Yes." We don't only hear what we want, in as much as motivation has zero direct control over the transduction of auditory signals in a sensory sense. Motivation affects which way we turn our ears and whether we keep them in a room with sounds we want to hear vs. a room with sounds we don't want to hear, but if those sounds hit our ears, whether we want to hear them shouldn't affect whether the stereocilia in our cochleae wiggle and tell our brains all about it. That's the only qualification of the otherwise plainly affirmative answer that occurs to me.

In a perceptory sense, motivation matters a lot more, because transfer from echoic memory to working memory is a matter of attention, and motivation certainly affects attention. E.g., if you're listening for a particular sound, you'll notice it better (hence the cocktail party effect), and you'll even experience more false alarms in the signal detection sense. A personal example within the general example: all the sounds that had the same pitch and tone as the first note of my cell phone ringtone used to drive me nuts when I would take a shower while anticipating a call from a girl I really wanted to talk to, who would often call me unexpectedly and complain when I didn't answer.

Transfer from working memory to long-term memory is arguably even more sensitive to motivation, because it depends greatly on elaborative rehearsal. Hence the more obsessed (or just interested) you are with a particular topic is the more often and deeply you'll think about it, and the more likely you'll remember it after your working memory's fairly short duration is up. If you don't remember something, you can't say whether you heard it, so the better you remember is also the more evidence you can offer that you have heard it. This is important in an empirical epistemic sense for our purposes, partly because it exacerbates the effect as perceived retrospectively, and thus reinforces the folk theory in your title.


Does nostalgia contribute to overrating past experiences?

The answer to this is most definitely a broad one. This depends on the persons experiences and how they take it all in. The answer before made a good point about happiness is defined differently among everyone. It’s up to you what you connect that with. Most people have a sentimental feeling when thinking about their family some might be completely opposite, maybe it’s because their family aren’t good to them and they were abused before by them or some sort of behavior to leave them with negative memories.
Life is strange and so are people. We have plenty of studies to explain this and so far people still seem to be lost without direction in their life.
great article you should take a look at
References
FioRito, T. A., & Routledge, C. (2020). Is Nostalgia a Past or Future-Oriented Experience? Affective, Behavioral, Social Cognitive, and Neuroscientific Evidence. Frontiers in Psychology, 11(1113). https://doi.org/10.3389/fpsyg.2020.01133


Comprehensive list of cognitive techniques in CBT

You might want to check out http://www.anxietyonline.org.au/ . It's free for the eTherapy version and is funded by the Australian federal government.

A colleague of mine gave a presentation and it looks really good. From the website:

  Anxiety Online is a comprehensive online mental health service
  offering information, assessment, online diagnosis and treatment
  programs ("eTherapy") for the anxiety disorders:-

Once you have gone through the the fairly long diagnostic process, you get access to a range of eTherapy resources. In particular, you can use it to learn more about CBT. It has exercises and videos.


Are there guidelines in the peer reviewing process on assessing methodology?

This does not really answer your question (because it doesn't deal in detail with methodological issues), but there is a nice journal article that deals with problems of the peer review process in general by evaluating "great scientific works of the past" from the perspective of current social sciences:

Trafimov, D., & Rice, S. (2009). What if social scientists had reviewed great scientific works of the past? Perspectives on Psychological Science, 4, 65-78. doi:10.1111/j.1745-6924.2009.01107.x Available online at http://cda.psych.uiuc.edu/writing_class_material/perspectives_articles/trafimow.pdf

The reference list has some articles on statistical/mathematical methodology questions.

In another interesting article, Gerd Gigerenzer shows how p-values are misinterpreted in current research and null hypothesis testing is made a false requirement for the acceptance of papers by major journals:

Gigerenzer, G., Krauss, S., & Vitouch, O. (2004). The null ritual: What you always wanted to know about significance testing but were afraid to ask. In D. Kaplan (Ed.), The Sage Handbook of Quantitative Methodology for the Social Sciences (pp. 391-408). Thousand Oaks, CA: Sage. Available online at http://www.sozialpsychologie.uni-frankfurt.de/wp-content/uploads/2010/09/GG_Null_20042.pdf

A Google search for "peer review guidelines" brings many hits from publishers and institutions. Maybe some of them deal with methodological issues in more detail.