What is the best unobtrusive and objective method to measure mental workload?

There are different parameters you can use, but as the question is not clear what exactly you want to do , I think with EEG and Task Load Index (TLI) you are good to go.

  The Task load index (TLI) is the so called engagement-index  and  is
  defined  by  two  formulas,  TLI1  and  TLI2. However, these indices
  were calculated as follows:

  where Pθ and Pα denote the theta- and alpha-band power, respectively.
  Pθ,Fz and Pθ,AFz are the theta activities of Fz and AFz electrodes
  respectively. The θ (theta) activity was calculated by averaging the
  power spectrum of the θ frequency range (4-7.5 Hz). Similarly, Pα,Pz
  and Pα,CPzPOz are the α (alpha) activities of Pz and the pool of CPz
  and POz electrodes, respectively. The α activity was calculated by
  averaging the power spectrum of the α frequency range (8- 12.5)

This section is exactly quoted from this paper.


Do Big 5 or BIS/BAS personality theories propose that combinations of personality traits are meaningful?

Here are a few ways of thinking about this:

Regression modelling - Main effects: When we predict an outcome of interest from multiple traits (e.g., the Big 5), we often get multiple significant parameters. For example, when predicting life satisfaction, low neuroticism and high extraversion tend to provide the strongest predictors, but there are also typically positive coefficients for the other factors. Thus, the coefficients imply a way of forming a personality composite to maximise prediction of an outcome.
Regression modelling - Interaction effects: You can examine interaction effects of multiple traits (e.g., is there a neuroticism by extraversion interaction in predicting life satisfaction). This is typically examined by including both the raw variables and the product of the two interacting variables. The significance of the product is used test for an interaction effect. That said, my general sense is that these kinds of interactions tend to be very small in comparison to the size of the main effects.
Type-based research: There are various conceptions of personality such as Type A and Type D personality. They often define a categorically distinct personality in terms of status on a number of traits. For example, Type D is defined as high negative affect and high social inhibition. Such type based approaches implicitly assume that it is useful and ideally meaningful to talk about such clusters of traits.
Higher level traits: Another way of thinking about correlated traits is in terms of an underlying higher level trait. This is proposed explicitly in hierarchical measures of personality such as the NEO-PI where there are 6 facets for each of the Big 5. Thus, the six conscientiousness facets are in some sense combined to form the overall conscientiousness factor (see facet versus factor prediction). In a less explicit, we can also see discussion of the Big 1 (a proposed higher level factor explaining some shared variance in the Big 5) as an implicit way of combining the Big 5.


Is there a neutral term for people who tend to avoid face-to-face or video/audio communication?

I agree with @AlwaysConfused that this sounds very like someone with Asperger's.

However, if you want a more "neutral" term, would Introvert help?

Such a person - an Ixxx on the Myers-Briggs scale - typically finds their "energy levels" drain when in groups of people, and recharge when they are on their own.


What is "synaptic polarity" in a chemical synapse?

From a paper on C.elegans:

  To understand the neural basis of these behaviors requires some information not only about the pattern and strength of the connections but also about the type of their synapses. The same neural circuit can perform different functions depending on the signs of synaptic polarities it contains. Specifically, circuits in which excitatory synapses dominate can sometimes become epileptic. On the other hand, networks with only inhibitory connections could be silent, and therefore in many situations useless. Thus, it may seem that some sort of an intermediate regime is necessary for a proper functioning of the nervous system

In that paper that's all they mean by it. It's not a very widespread term, and should not be confused with [the much more widespread term] neuronal polarity, which means the differentiation between dendrites and axon as the neuron develops. Also of note that synapses can also be classified morphologically, and when doing that there are more than two types, e.g. S-type, F-type and C-type.


Spurious attractors in Hopfield networks

I think that your intuition about the lower "energy ratio" of spurious states explaining their greater susceptibility to unlearning might be correct.

In a Hopfield Network spurious states are activity patterns that have not been explicitly embedded in the synaptic matrix, but are nonetheless stable. They are in other words "unwanted" attractor states that, by virtue of a finite overlap with the "wanted" attractor states, come about as a local minimum in the energy function. The unlearning rule in Hopfield et al. (1983) consists in modifying the synaptic matrix so as to decrease the energy of the stable states in which the network dynamics settles down, be them spurious or embedded states. Because the spurious states have higher energy than the embedded states, they are more strongly affected by the unlearning step.

Now, why do spurious states have higher energy than the embedded attractor states? Well, this is actually not true in general, but it is the case in a regime where the Hopfield network doesn't exceed its loading capacity, that is when the number of learned patterns over number of units $p/N$ is lower than the critical capacity $\alpha_c\approx0.138$. In this regime, it is possible to estimate the overlap of the spurious states with the learned patterns, and show that is generally lower than $1$ (the overlap of the learned patterns with themselves). Because of how the Hebbian construction of the synaptic matrix in the Hopfield model, this overlaps are terms that appears in the energy function. The energy of a pattern is namely proportional to minus the square root of its overlap with the learned patterns. This means that the spurious patterns have higher energy than the learned ones.

In general this kind of naive considerations has to be supported by more rigorous arguments based on probability theory. These for instance point out that even for the regime below $\alpha_c$ the retrieved patterns are actually spurious states as soon as the number of embedded patterns $p$ exceeds above $\frac{N}{2\ln N}$. Such spurious states have however such a high overlap with the learned patterns ($0.97$) that they basically coincide with them.

This result and generalizations thereof for non-zero temperature (i.e. noise in the dynamics) and beyond critical capacity have been worked out in the following very technical paper:

Amit D.J, Gutfreund H and Sompolinsky H (1987) Statistical Mechanics of Neural Networks Near Saturation. Ann. Phys. (NY) 173, 30

and in the book:

Amit D.J, (1992) Modeling brain function: The world of attractor neural networks. Cambridge University Press, ISBN:9780521421249


How to improve working memory in adults?

IQ is not the same as working memory (either visual or non-visual). IQ is deprecated in favor of the term general intelligence (g).

Education improves g, but not by much; only about one point per year of education (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4445388/), where about 15 points are a standard deviation.

Many things affect general intelligence negatively, such as lead exposure or inadequate nutrition. However, once basic good conditions are experienced, cognitive decline is not avoidable. The good news is that while g decreases in older adults, semantic memory (knowledge) can continue increasing, such that real-world performance on many tasks need not suffer.

Beware a huge range of companies and hucksters promoting activities to slow cognitive decline: to my knowledge, none of them have much validation nor a consensus of scientists without conflicts of interest (e.g., financial).


I only know of one Cognitive Model dividing the unconscious and conscious mind is presented by Paul Thaghard in "Two theories of consciousness: Semantic pointer competition vs. information integration". I explain this model in layman's terms in my blog post. In this answer, I'll compare Thaghard's model to Yate's model you've presented above.

Yate's model is based on the ideas of Global Workspace Theory (GWB). GWB posits that unconscious processes compete for the spotlight of attention so that they can enter consciousness. This seems to be what Yate's is suggesting in this diagram and would tie in nicely with mindfulness meditation.

GWB isn't a bad model. It makes a few predictions and describes a lot of phenomena (comas, certain types of blindness). However, it's not easily testable or disprovable. How do these unconscious processes interact? What type of representation would unconscious processes use and how does this relate to neurons? Can I build a computation model of consciousness based off this specification? These are the things that Paul's model worries about and specifies. Paul's model is essentially a more specified version of the Yate's model. It defines a representation (Semantic Pointers) which relates to neurons and makes testable claims.

To summarize and get back to your question, Yate's model is vaguely consistent with Cognitive Science, but it is under-specified. For further reading on more specific models, check the links in this answer.


Do people who experience a psychotic episode ever go back to normal?

Short answer

Because some neuroses can involve psychotic episodes, it depends on the cause of the psychotic behaviour.

Longer Answer

When looking at the difference between neuroses and psychoses, although BPD, Bipolar Disorder and PTSD are generally neuroses, they can involve psychotic episodes in some cases.

For example, with Bipolar Disorder (Mind, 2018):

  Psychotic symptoms can include:

  delusions, such as paranoia
  hallucinations, such as hearing voices

  Not everyone with a diagnosis of bipolar disorder experiences psychosis, but some people do. It's more common during manic episodes, but can happen during depressive episodes too. These kinds of experiences can feel very real to you at the time, which may make it hard to understand other people's concerns about you.

Psychotic episodes in Post-Traumatic Stress Disorder (PTSD) can involve flashbacks (the sense of being back at the traumatic event) through hallucinations affecting touch, taste, smell, sound and sight either affecting one of the senses or a combination of them.

Once the PTSD or Bipolar Disorder has been resolved through the relevant treatment required, the psychotic effects will not return as the underlying cause has been sorted, and the person will "go back to their pre-psychosis self".

If the psychosis is a "pure" psychosis such as Schizophrenia, the problem cannot be cured, but the psychosis can be managed with medication and psychiatric help (Schizophrenia Society of Canada, n.d.).  Schizophrenia requires lifelong treatment, even when symptoms have subsided (Mayo Clinic, 2018).

Minimizing the impact of the illness depends mainly on early diagnosis and, appropriate psychosocial treatment and medication.  One problem with this is that people with schizophrenia sometimes lack insight into their illness, and therefore do not see the need for medication or other mental health help. Also, medication sometimes has unpleasant side effects and this may discourage individuals from continuing to follow their prescription.

References

Mayo Clinic (2018). Schizophrenia Diagnosis & Treatment[Online]Retrieved from: https://www.mayoclinic.org/diseases-conditions/schizophrenia/diagnosis-treatment/drc-20354449

Mind (2018). Bipolar Mood Symptoms [Online]Retrieved from: https://www.mind.org.uk/information-support/types-of-mental-health-problems/bipolar-disorder/bipolar-moods-symptoms

Schizophrenia Society of Canada (n.d.). Frequently Asked Questions [Online]Retrieved from: http://www.schizophrenia.ca/faq.php


Implicit Learning

  Implicit learning refers to situations in which complex information is
  acquired effortlessly (without a conscious effort), and the resulting
  knowledge is difficult to express verbally. (Italics mine)

As discussed in the Wikipedia page, the exact definition is controversial, but all the paradigms (verbal reports, forced-choice tests, etc.) listed, the knowledge is gained unintentionally and without awareness.

Both these criteria relate to the learner's subjective relationship with the acquired knowledge. It says nothing about behavior and reinforcement, which may be readily apparent.

Consider social skills as an example. I may smile, gesture, and make eye-contact appropriately (behavior), and I experience positive social outcomes when I do so (reinforcement). However, I never explicitly set out to learn the number of milliseconds to maintain eye-contact, or what situations warrant a smile. Moreover, if someone offered to pay me to write instructions on how to engage socially, I would have a hard time articulating my knowledge. It is implicit.

Latent Learning

  Latent learning is defined as learning that occurs in the absence of
  any obvious reinforcement or noticeable behavioral changes. (Italics mine)

These criteria relate to the objective behavior and circumstances of the learner. It says nothing about the learner's subjective awareness of the knowledge.

Consider the bus ride example. I may be perfectly aware that I am gaining knowledge of the bus route through observation. But an objective observer would have no way of proving that I have learned the route: I behave the same as if I had not learned it, and I receive no clear reinforcement for doing so. However, if someone offered to pay me to give directions to my work place, I would be able to do so. My knowledge is explicit but hidden.

To sum it up very roughly:

Implicit learning is when the knowledge you gained isn't apparent to you.
Latent learning is when the knowledge you gained isn't apparent to others.


Here is a comprehensive list of Computational Neuroscience Software

My opinion below comes form the perspective of nonlinear dynamics (using differential equations to model ion currents in neurons).  So more the math/physics/electrical engineering approach to Computational Neuroscience (not so much the Computer Science or Psychology approach):

Personally, I don't use pre-packaged tools like NEURON or GENESIS.  I take mathematical models established in literature (i.e. The Hodgkin Huxley model) and use Matlab or Python to model them.  I essentially do what Neuron or Genesis does, but I do it my way so I can extract the information that's relevant to me.  This is how I have been trained through physics and applied mathematics departments.  To not rely on other people's implementations.

For nonlinear analysis of dynamical systems (because there's really a lot of extravagant mathematics that you don't want to just code yourself) a lot of people use XPP/AUTO, designed, in part, by Bard Ermentrout (a well-known computational neuroscientist).  This is a good way to go if you're not into writing code, but I prefer a more hackable tool.  I've been learning Matcont, a similar toolbox for Matlab but since it is made with m-files (matlab's data type) you can hack it and make it into code to integrate with your own Matlab software, avoiding the GUI clicking and dragging.


Are there any free online questionnaire/survey sites that also measure the time it takes for participants to answer each question?

Here are a couple of suggestions:

Inquisit records the timing of each response and can be run online.
If you care about timing a lot and you need to run the study online, then this is quite a good option.
Qualtrics can record various features of survey delivery time. In particular, you can record time spent on each survey page. If you have one question per page, this can approximate time to respond to the item. This can be useful if you want to identify participants who are not reading items. However, I wouldn't use Qualtrics for cognitive reaction time based experiments. Note also that in order to record item response times you need to manually set this for each survey page.


Can people alleviate a negative halo effect about them?

A halo effect suggests that the overall impression of a rated object (e.g., a person) excessively influences the impression of facets of a person. This leads to correlations between facet ratings higher than would be expected were facets rated accurately.

If someone is a nearly perfect person, then presumably the overall impression they create would be very positive. The halo effect would not influence this overall very positive rating. It will merely increase ratings for facets that should be rated below the overall rating and decrease ratings for facets that should be rated above the overall rating..

Worked example:

Let's simplify it and assume that your person's true rating on all the facets that matter  out of 10 are:

Facet A = 6
Facet B = 10
Facet C = 10
Facet D = 10

If we further simplify to say that overall impression is just the mean of the facets, we have overall impression of (6+10+10+10)/4 = 9.
So, an example of a rater influenced by the halo effect would be one who gave rating such as:

Facet A = 9
Facet B = 9
Facet C = 9
Facet D = 9

or

Facet A = 8
Facet B = 9.33
Facet C = 9.33
Facet D = 9.33

Conclusion:

The point is that facets that are worse than the general impression are pulled up, and facets better than the general impression are pulled down. The mean of the facets has not changed. It is just the accuracy of facet ratings has declined.  While this is an idealised example, the question relates to a theoretical effect.

A classic examples of a halo effect is where a teacher is marking an assignment and each section of the assignment is graded. If the teacher is influenced by halo effect then the overall mark is not influenced, but the rating for each section will be less differentiated than it should be. So from a quality of student feedback perspective, this is worse, but from a grading perspective, it makes no difference. That said, we might hypothesise that raters that exhibit halo effect may also exhibit other rating problems.

Second guessing your question, perhaps you are interested in some other biases such as first impression bias, central tendency bias, or generally inaccurate ratings. Or perhaps you are, rightly or wrongly, assuming that the overall impression would involve an inaccurate implicit weighting of facets.


Are there neural loops within a column or an area of the cortex?

I've read evidence for single-neuron, two-neuron, and larger loops/cycles throughout the cortex, including intralaminar, interlaminar, and interareal neural loops. But it would take me far too long to back that statement up.

Instead, I offer a list of papers to get you started. I've read all these papers, and they all provide evidence for neural loops in the cortex, especially two-neuron loops. Within these papers, search for "loop", "reciprocal", and, if you're interested in single-neuron loops, "autapse".

References

  Alonso, J.-M. (2002) Neural Connections and Receptive Field Properties in the Primary Visual Cortex. The Neuroscientist. 8(5):443-456
  Feldmeyer, D. (2012) Excitatory Neuronal Connectivity in the Barrel Cortex. Frontiers in Neuroanatomy. 6(24):1-22
  Rockland, K.S. and Knutson, T. (2000) Feedback Connections from Area MT of the Squirrel Monkey to Areas V1 and V2. The Journal of Comparative Neurology. 425:345-368
  Thomson, A.M., West, D.C., Wang, Y., and Bannnister, A.P. (2002) Synaptic Connections and Small Circuits Involving Excitatory and Inhibitory Neurons in Layers 2-5 of Adult Rat and Cat Neocortex: Triple Intracellular Recordings and Biocytin Labelling In Vitro. Cerebral Cortex. 12:936-953


Are there ways to accelerate the recovery from depression via novel pharmacological antidepressants?

Wikipedia maintains a list of potential antidepressants currently under investigation.

Of some note, the US FDA recently approved esketamine for clinical use.  After being banned in the 1970s, psychedelics have become available for research purposes again in the past 20 years or so.  Esketamine, a derivative of the psychedelic drug ketamine, which was already approved as an anesthetic, is an early result of this resurgence.  Other psychedelics (eg, psylocibin, LSD, mescaline, DMT, MDMA) are being investigated as potential treatment for a variety of mental disorders, including depression.

Also of note, transcranial magnetic stimulation (rTMS) is a relatively new treatment for some types of depression.  The notion that depression comes in several forms or sub-types, responsive to different treatment options, has lead to the investigation of a variety of genetic tests that may help personalize treatment in the future.  Additionally, several labs (example) are investigating the possibility of using fMRI to distinguish such sub-types using brain scans.


Can drawing a duck define a person's hemispheric dominance?

What is the dominant hemisphere in the first place? I found the following definition (source: Medical Dictionary):

  [The] dominant hemisphere [is] [t]he left half of the brain in almost all right-handed people and 85% of left-handed people. This is the hemisphere concerned with language and logical thought and containing the motor areas for voluntary use of the right side of the body. In 15% of left-handed people, the right hemisphere is dominant and subserves speech.

Now, your ducks facing left or right hardly seem to reflect either language, logic, motor lateralization or handedness. Instead, often questionnaires or inventories are used, for example to tease out whether a person is logical, rational and verbal (left-sided); or emotional, manipulative/spatial and creative (right-sided). However, the meaning, relevance, and possible use of hemispheric dominance is debated.

Note that brain lateralization is certainly true for a number of functions, including speech and motor control, but the more dramatic examples of brain lateralization should be interpreted with caution, and I quote from Corballis (1980):

  Since ancient times, right and left have been associated with different fundamental classifications, including male and female, good and evil, day
  and night, straight and crooked. [...] Interpretations of cerebral asymmetry that emphasize a fundamental duality in cognitive processing between the two sides of the brain, or that locate consciousness in the left side only, are probably modern manifestations of the age-old mythology of left and right.

Reference
- Corballis, American Psychologist (1980); 35(3): 284-95


Is it possible to detect the mental flow state with EEG?

Bearing in mind the fact that I can't prove a negative, I'm going to say "No, it's not (yet) possible".

Flow is rather loosely defined (e.g. "merging of action and awareness"), so coming up with hard measures is a challenge in and of itself -- even without bringing electrophysiology into the equasion.  As a Positive Psychology concept, it belongs to the realm of "soft science" psychology, and this tends to make fuzzy things stay fuzzy.  (Please note that I'm not using "soft science" pejoratively).

I think the best you can do is measure correlates of alertness and attention (e.g. look for desynchronization in the alpha band).  If you come up with a very clever design, you might even be able to elicit ERP components related to conscious awareness of a stimulus of interest (e.g. P300b complex), but even that will be very difficult in non-laboratory conditions.

Alternatively, you could turn to machine learning to search for patterns associated with the conscious processing of a stimulus of interest.  If you want to go that route, I'd strongly encourage you to read one of my colleagues' Ph.D dissertation [1].  This dissertation proposes some novel approaches to pattern classification with EEG (and MEG/iEEG).  Note that this problem is a much easier one (classification of non-communicative patients).  That, along with the insane amount of noise you're likely to get and the need for a very inventive design, earns you a hearty "good luck" ;)

Characterizing the Electro-magnetic Signatures of Conscious Processing in Healthy and Impaired Human Brains


Do people "subvocalize" during thinking or "internal monologue"?

Short answer
Sub-vocalization can also be detected during cognitive demanding tasks other than reading.

Background
As far as I can see, most literature acknowledges sub-vocalizing as being only detectable by measuring the electrical nerve activity that drive the speech organs (e.g., Parnin (2011) and NASA Research). When people perform complex tasks, these sub-vocal utterances can be recorded as electrical signals sent to the tongue, lips, or vocal cords, and these can be detected.

Sub-vocalizing has been mostly described in terms of reading (e.g. Slowiaczek & Clifton, 1980). Nonetheless, more recent literature also associates and acknowledges sub-vocalization when people perform mental tasks that claim a lot of mental processing, such as software programming (e.g., Parnin (2011), so the answer to your question is yes, it also occurs during thinking.

Interestingly, as a side note, stutterers sub vocalize more slowly, reflecting the fact that indeed much of the same mechanisms are at work during sub-vocalization as during normal speech (Bosshardt, 1990).

References
- Bosshardt, J Speech Hear Res (1990); 33(4): 776-85
- Parnin, IEEE 19th International Conference on Program Comprehension (2011)
- J Verbal Learning Verbal Behav (1980); 19(5): 573-82


What are the key dates for the development of operant conditioning?

It would have been pretty strange for there to be multi-year gaps in Skinner's publication record, and in fact, Skinner continued to publish every year in both of those periods and beyond (Epstein, 1977). I've provided a link to a list of his publications which includes both periods, but there is no real way to say which of these publications were the 'key' studies for operant conditioning. Hopefully, this will still be of some help.

References

Epstein, R. (1977). A listing of the published works of BF Skinner, with notes and comments. Behaviorism, 99-110.


I don't know if there is a name to this type of experiment, but this basically sounds like a test of recognition memory.

The features that subjects focus on would depend entirely on the task. If you ask them to match volume, they would pay attention to volume. If you ask them to detect a frequency match, they'll focus on pitch. If you run an experiment without specifying a feature, humans generally tend to weight the different features according to their reliability (signal-to-noise ratio). So if pitch is more informative in detecting a match, they would focus largely on pitch.

For example: https://link.springer.com/article/10.1023/A:1026557704054


Probably both a combination of being more tired and fewer distractions. Most other people will be asleep during the night. Programming is adversely affected by context-switching, thus night-time with stimulant-enhanced soda is more likely to provide you with long periods of interruption free coding.

Update: The above situation creates the conditions where Csíkszentmihályi's Flow is most likely to take place.


What is the effect called whereby people don't offer help when in a crowd because they assume someone else will help?

It's called the bystander effect:

  The bystander effect, or bystander apathy, is a social psychological
  phenomenon that refers to cases in which individuals do not offer any
  means of help to a victim when other people are present. The
  probability of help is inversely related to the number of bystanders.
  In other words, the greater the number of bystanders, the less likely
  it is that any one of them will help.

It was highlighted by the Murder of Kitty Genovese, which is part of the negative image of New Yorkers as apathetic, and is therefore sometimes also called "Genovese syndrome".

The bystander effect is a sub-type of Diffusion of responsibility.


Longitudinal mobile mood tracking app with random reminders

The best thing I can find is somebody's side project on experience sampling (the code is on github), so not sure if it's being maintained or anything, but it does appear to do exactly what you want.


What information does the connectome actually contain?

Well, regarding this short definition of a connectome from Wiki:

A connectome (/kəˈnɛktoʊm/) is a comprehensive map of neural
connections in the brain, and may be thought of as its "wiring
diagram". More broadly, a connectome would include the mapping of all
neural connections within an organism's nervous system.

Therefore you could read out all information, assuming you have enough computational power. (A perfect connectome would represent all information processes in the brain. Because processing information through connections is all the brain does, right? :D)
In the real world however, we need 'models' as simplifications to deal with these phenomena. A connectome is nothing else than such a model.
Influential Factors to consider

To make predictions of real-world constructs, you need to assess real-world phenomena. F.i. you need to have
postulated some outcome-variables (for lets say Schizophrenia) that need to
be quantified in the real-world (external validity) to be related to
inner-brain processes. These real-world concepts of psychological
processes, speaking of the behavioral, emotional and cognitive
aspects (which can be measured), are inherently fuzzy, which raises
the question, to which certainty we will be able to predict
psycho-physiological correlates.

Not to forget, memories are mainly coded as 'processes over-time',
something like chains of activation (other than distinct anatomy and
brain-areas who would define thoughts). Also noisyness and
randomness is always a variable you need to consider. (I think the
Hippocampus functioning of neurons induces randomness by design, but
I have no source right now.)

Also to mention:
The individuality of brains leads to decreased prediction of the model or a general model that would hold for every individual

The plasticity of the brain states states the ability to change and
evolve over time.  (Concepts like Imprinting and so on). A static
model might also not be sufficient to represent these (also highly
individualized) processes.

Situational- or environmental dependency also influences your
current state of mind. (It is not possible to 'control' all
environmental factors, unless you had infinite computational power.)

Also the brain and toughts are highly self-/auto-activating, recurring and in parallel.
Millions of neurons firing at the same time and oscillating in
rhythms. Thoughts that become conscious might only be the tip of the
iceberg in a sea of thoughts that are below a certain threshold.

My proposal to your question: "What exactly can you get from a connectome?"
In principle everything is possible, but practically we might never truely decode everything from a philosopical and mathematical point-of-view (we needed to create a perfect connectome, which would be a perfect simulation of the entire brain). We might however be able to find very accurate brain-markers that help in predicting real-world concepts that seem relevant for humans :)
Resources
Because it is great: Video of synchronizing fireflies
Buszaki: Rhythms of the Brain is a nice read on some how information is created in the brain and different processes


How to install MARSBAR toolbox in SPM12?

Thanks for the comments, @serk1. The answer to this question is that that is a bug, it seems.

I gave up editing the scripts myself and decided to reinstall Matlab and Marsbar, and it properly recognized the path and the permission for the files after that.

I will leave the question here, in case someone run into similar problems.


What are the temporal limits of the auditory system?

As far as I know, auditory clicks are the shortest possible auditory stimuli. The shortest auditory click I was able to find in the literature, and which was used in a psychophysical context (i.e., audible to a human) was 10 microseconds (Leshowitz, 1971).

The longest sound we can hear is pretty much defined as a human's maximum age I guess. While the auditory system definitely adapts to acoustic stimuli at the neurophysiological level (Pérez-González & Malmierca 2014), this neural adaptation does not become evident in gross psychophysical adaptations. In other words, prolonged acoustic stimulation does not lead to sounds becoming less audible, let alone inaudible. That, because tonal stimuli consist of continuously changing air pressure differences. Of course, a continuous pressure applied to the eardrum is not heard, but a stimulus like that is not sound, but simply pressure, as it has no tonal content.

References
- Leshowitz et al. J Acoust Soc Am 1971; 49, Suppl 2:462-6
- Pérez-González & Malmierca, Front Integr Neurosci (2014); 8: 19


The idea that long term memory cannot be ever changes is absolutely wrong, for sure some thing that is learnt and practice for a long time while being a child has a difficulty to change after while, but it is not impossible.

About learning you have to know that we have different kind of learning disabilities.

  Specific learning disorder is a developmental disorder that begins by school-age, although it may not be recognized until later. It involves ongoing problems learning key academic skills, including reading, writing and math.

These patient usually can learn about everything but for specific type they have a difficulty learning. Based on what their difficulty is, they might get different treatment. Diagnoses is not also easy in some cases, for example patient who has difficulty learning math might be because of his difficulty reading text so if you try teaching math only by images and art and symbols he can learn.

reference here.


Do separate neural circuits express separate genes in the same type of brain matter?

So, I am revisiting your question as asked by community, and I discover I misunderstood it initially: you didn't say neurons process information, you said neural circuits do. And that distinct neural circuits process separate forms of information. Well, that is inexact. There are several types of neurons, adapted to create neural circuits able to process motor, sensory and a combination of the two. Here's a jolly picture of some of them from here   :

As for your question itself, it is quite confusing, at least at the level of knowledge of the brain we have at the moment: Do separate neural circuits express separate genes? We hardly know the surface of how the brain works, we consider a great improvement in science the fact that the psychotic spectrum gene pool has been somewhat mapped .

However, to somewhat answer your question, for example,  there is a gene  that is sometimes (not always) involved in Tourette syndrome and has been studied. The main idea is that "The SLITRK1 protein probably plays a role in the development of nerve cells, including the growth of specialized extensions (axons and dendrites) that allow each nerve cell to communicate with nearby cells. " Now, Tourette's  might be associated with Altered parvalbumin-positive neuron distribution in basal ganglia, which could be either the result of SLITRK1 gene mutation, or some other gene.

Let us put it this way: we do not have genes that suddenly create a third arm or a second heart, so we shouldn't have genes that suddenly create the wrong kind of neurons in the wrong region of the brain (I suppose that's what you mean by "type of brain matter", region of the brain, as neurons are generally all on the same level of the brain matter).

My best hunch, judging by the research I presented above, is that gene mutations might encourage or discourage the development of the type of neurons you'd expect in certain areas, which improves or disables the ability to process this or that type of information. Same as above, expressions of the genes involved in making this or that protein or physiological process that favors development of neurons in very specific areas of the brain - will also influence the way or intensity we process information with that specific region of the brain.

But - and it's a revelation I had myself while documenting this answer - genes do not express or suppress neuron development directly. The brain is what it is, and has the same format , if you will, no matter whose you dissect.

Genes influence metabolic and general physiologic process that are also part of the brain development. Your brain regions will process better or poorer due to the types of proteins that trigger development for the neurons, neurotransmitters that control the electric flow through the etc involved in the matter. Neural cells are hard-coded. Their development and functioning aren't.


Explanatory gaps in the formation and propagation of action potentials

I will try to answer all of your main and sub questions structurally below:

How do neurotransmitters manage to depolarize the inside of the cell?

Do they force the cell to give up pumping out Na ions?
No, the Na,K-ATPase (the sodium potassium pump) keeps active, also during the action potential (AP).
Do the neurotransmitters themselves contain positively charged ions that the ion pumps are not sensitive to?
They can, but neurotransmitter charge is irrelevant.
Answer: Neurotransmitters bind to their corresponding receptors. An example excitatory neurotransmitter is glutamate (Glu). Glu has many receptors and one of them is the NMDA receptor. The NMDA receptor is coupled to a cation channel that opens when Glu binds (and other conditions pertain). In turn Na+ and other depolarizing cations can enter the cell through the open channel. Other neurotransmitters and receptor mechanisms exist, but the coupling to a cation channel is a commonly encountered theme.

When the cell depolarizes, the electrical impulse travels down the axon. When this happens, Na+ and K+ ions rapidly pass through the membrane as the signal fires. [...]

Why are ions being pumped in and out of the axon in such a way to propagate an action potential?
During an action potential, the voltage changes are not the result of ions being pumped in or out of the cell. Instead, ions flow along their concentration and charge gradients out or in the cell during an action potential. For example, Na+, a key ion in any action potential, flows passively into the cell during an action potential. Passive influx occurs, because Na+ is continuously and actively pumped out of the cell into the extracellular fluid by the Na,K-ATPase. Moreover, the inside of the cell is highly negatively charged. Both the concentration gradient and charge gradient (i.e., the potential difference) will cause Na+ to surge into the cell once Na+ channels open. How then does it move across the axon? The trick is that Na+ depolarizes the cell membrane. When for example Glu binds to its NMDA receptor, Na+ enters the cell into the dendrite. Then, voltage-gated ion channels take over. Voltage-gated ion channels open or close depending on the local membrane potential. Most notably, voltage-gated sodium channels (VGSCs) open when the cell membrane depolarizes. Hence, after NMDA receptors are activated in the dendrite, Na+ enters. This in turn depolarizes the dendrite and VGSCs open. This causes further depolarization and adjacent VGSCs open etc. etc. Voltage-gated potassium channels open after the VGSCs and re-polarize the membrane. An overview is provided in the following image from Antranik.org :

Why isn't it just a positively charged signal running through the axon, without regard to the outside environment?
Charges only move to an opposite charge. A neuron is not differentially charged from dendrite to axon terminal. Hence another way of action potential transduction is needed. Step-wise opening of VGSCs is a clever trick to use a constant cell membrane potential to generate a directional action potential.


Could physically simulating neural structure on a fundamental level yield superior results to machine learning algorithms?

Very interesting question. Although I have not a single little bit of expertise in this area, I do have some references you may want to read. First is a paper by Merz and Fromherz (2005) where they grew snail neurons on a silicon chip. Pfister et al (2007) also tried to grow neurons to allow interfacing between neurons and machine (for neural prosthesis e.g.). There is thus definitely a field of research that believe neural interfacing may be better than mechanical and algorithmic networks.

There has been 10 years worth of research since these papers so I bet there are some advancements that may give you a more definitive answer than mine.


Can new emotions be created or discovered?

The atlas of personality, emotion and behaviour catalogues over 3,000 emotions (Mobbs, 2020).  The atlas's approach taken to identifying and cataloguing the emotions was to start with existing lists of emotions and then using thesauri to identify synonyms and antonyms of emotions, which are themselves likely to be emotions.

I expect that over time, existing emotions will be subdivided into more specific variants which will then need to accepted by the curators of each dictionary.  At the point these variants are included in dictionaries, the new emotion will be deemed to discovered.

Mobbs AED (2020) An atlas of personality, emotion and behaviour. PLOS ONE 15(1): e0227877. https://doi.org/10.1371/journal.pone.0227877


Do dissatisfaction with a job and relationships share the same mental mechanism?

In general, personality traits correlate with most measures of satisfaction. Most notably, there is a large literature showing that personality correlates with life satisfaction (see Steel et al). In general, neuroticism is the biggest correlate followed by extraversion and conscientiousness.

The following table from Grant et al summarises two major meta-analyses on the correlation between big 5 personality and various measures of well-being including life satisfaction:

From a theoretical perspective, personality represents an interpretative lens through which people experience the world. Some people are generally more positive or more negative. Some people focus on problems, others focus on what they have. Of course, eve

Personality and Job Satisfaction

I've seen similar correlations looking at personality and job satisfaction (see Judge et al), although in general these correlations are smaller than for life satisfaction. This may reflect the greater role of context. Here is the table of meta-analytic correlations from Judge et al between big 5 personality and job satisfaction.

Personality and Relationship Satisfaction

Here is the meta-analytic estimate of the correlation between personality and intimate partner relationship satisfaction from Malouff et al (2008).

General Comments

In general, the two tables above look somewhat similar to each other. Neuroticism correlations are the largest in both (r = -.22, r = -24).
However, extraversion and conscientiousness may be slightly more relevant to job satisfaction.

References

Grant, S., Langan-Fox, J., & Anglim, J. (2009). The big five traits as predictors of subjective and psychological well-being 1.Psychological reports, 105(1), 205-231.
Judge, T. A., Heller, D., & Mount, M. K. (2002). Five-factor model of personality and job satisfaction: a meta-analysis. Journal of applied psychology, 87(3), 530.
Steel, P., Schmidt, J., & Shultz, J. (2008). Refining the relationship between personality and subjective well-being. Psychological bulletin, 134(1), 138.
Malouff, J. M., Thorsteinsson, E. B., Schutte, N. S., Bhullar, N., & Rooke, S. E. (2010). The five-factor model of personality and relationship satisfaction of intimate partners: A meta-analysis. Journal of Research in Personality, 44(1), 124-127.


Along with many others, Google Scholar came up with the following articles for me

American Association for the Advancement of Sciencetalks about the relationship between health and a sense of control old age
National Academy of SciencesExperimental and economic studies suggest large-scale programs aimed at self-control to improve citizens' health could reap benefits
International Association of Applied Psychology
Self-Regulation Assessment and Intervention in Physical Health and Illness: A Review
Book - The Self-regulation of Health and Illness Behaviour


Is there any (free) program that allows the recording of text input and the speed of input?

I imagine most software designed for creating psychological experiments will be able to do this. (e.g., EPrime, Direct RT, MediaLab, SuperLab, etc.). I've mainly used Inquisit to record responses and response times. These are all proprietary options.

You could also readily implement a trial interface with a textbox and response times in standard programming languages. For example, I've used visual basic on occasion to record data in textboxes.

Finally, as @Dan M mentions there is psychopy which is free. I have not personally used it.


I think you need to think about what you mean by "speed of thinking".
Your language implies that you are looking for a generalised way to be more intelligent. I have not seen any simple interventions for increasing general intelligence.

You may find it more productive to focus on particular domains of your life that you want to improve. Practice and instruction improve performance in a given domain. There are a wide variety of mechanisms by which this occurs, some of which could be characterised as speed of thinking.

In particular, practice often leads to automaticity. Take for example, learning your times tables. When you first encounter a given question (e.g., 8 * 8 = 64), you may have to use a longer algorithm to solve the problem, but with practice, the equation itself may directly trigger recall. Alternatively, take many computer based tasks. The first time you try to perform a task (e.g., sorting your email by date), you may have to think more about how this task can be performed. With practice, you just recall how to do it.
A similar process of automaticity also applies to the perceptual and motor domains as you learn to assign visual attention effectively or learn to smooth out motor responses (for a review see Rosenbaum et al 2001).

This process of acquiring automaticity in a given domain is not exactly speed of thinking, but it has the same consequences. Automated actions reduce the demands on limited attentional resources, and can be executed quickly and efficiently.

For specific suggestions on what makes a great practice schedule you may want to read up on the literature on deliberate practice (e.g., Ericsson, et al 1993).

References

Ericsson, K. A., Krampe, R. T., & Tesch-Römer, C. (1993). The role of deliberate practice in the acquisition of expert performance. Psychological review, 100(3), 363. PDF
Rosenbaum, D. A., Carlson, R. A., & Gilmore, R. O. (2001). Acquisition of intellectual and perceptual-motor skills. Annual Review of Psychology, 52(1), 453-470. PDF


What is Attention Deficit Disorder on adults and how is it treated?

It doesn't sound like your just looking for some general info about the psychological disorder of ADHD. The thing you should maybe start out with is understanding that there are two different sub-types which will have different effects.

Rather than explain everything, I would point you to a couple links that should answer your questions:

For a basic definition you can look at the CDC page on ADHD.

Here is some basic info that should get you started on understanding the disorder.

wikipedia should fill in anything else that you want to know, if you have a more specific questions, feel free to ask.


What is the learning/memory type which requires active contribution called?

Short answer
This type of engaged learning is referred to as active learning.

Background
In contrast to the traditional, mostly passive ways of teaching (one-way lecturing), nowadays there's a trend to active learning.

  Active learning is any approach to instruction in which all students are asked to engage in the learning process. Active learning stands in contrast to "traditional" modes of instruction in which students are passive recipients of knowledge from an expert.

Markant et al (2016) explain in a review article that active learning leads to better outcomes than passive forms of instruction. They summarize that the opportunity to control the information while learning leads to improved memory. Mechanisms involved in this effect include the formation of sensorimotor associations, adaptive selection of material and metacognitive monitoring.

Active control over a learning situation results in large areas of the brain being recruited and interconnected during active exploration (source: Psych Central). For example, active exploratory behavior during the observation of objects enhances memory recall (Voss et al., 2011), resulting in enhanced activity in the dorsolateral prefrontal cortex, the cerebellum and the hippocampus is higher and more coordinated after active learning (source: Illinois News Bureau).

References
- Markant et al  Mind, Brain, and Education Society (2016); 10(3): 142-52
- Voss et al., Nat Neurosci (2011); 14(1): 115-20


Is there a name for a scientist's resistance to disconfirmation of his or her theories?

This isn't quite what you are looking for, but it's close enough that it might help you find additional information.

Munro (2010) found evidence that people tend to discount the scientific possibility of studying something when presented with scientific evidence that goes against their current beliefs. In other words, if people were shown a result that went against their beliefs, then people were more likely to conclude that it was not possible to conduct rigorous scientific experimentation on the topic. He called this the scientific impotence excuse. In the experiment, subjects were shown an (artificial) abstract that claimed there was either a link between homosexuality and mental illness or claimed there was no link. A control group saw the same abstracts, but instead of a link between homosexuality and mental illness, the link was between a made-up group like Zavs. After reading the abstract, subjects were asked to indicate whether or not it was possible to investigate such links with scientific methods. If the results of the abstract were contradictory towards a subject's prior beliefs (as measured by a questionnaire at the start of the experiment), then the subject was more likely to say that the question cannot be investigated in a scientific manner.

This study was done with college students, who are not trained scientists, so it's unclear whether the result would generalize to scientists or not.


Although there is a robust science of animal behavior, it's very difficult to determine what kinds of experiences or thoughts animals are having. In short, we can only observe their behavior. Philosophers argue that a "zombie" or a robot could also demonstrate exactly the same behaviors but have no mind behind them, which means that we can't infer the thoughts just from the behaviors. We can't measure the thoughts themselves. Even neural activity is just a proxy; they are not the thoughts. Frans de Waal's recent bestseller goes into great depth on animal emotions and suggests that there are no uniquely human emotions; I'm guessing he would think that your cat understands you as an agent and has loving feelings towards you.  https://www.nytimes.com/2019/02/25/books/review/frans-de-waal-mamas-last-hug.html


Is the Wonderlic invalid if you have previously done other intelligence tests?

It is assumed that most people taking intelligence tests have been exposed to a wide range of assessments in the past. It is a standard feature of education systems that students will do a wide range of assessments, and some of these are more or less like intelligence tests.

Many tests even have practice questions for the purpose of increasing validity. The rationale is that some people may perform unnecessarily poorly because they're not familiar with the interface or the general test taking strategy.

So, no, doing another intelligence test doesn't invalidate your current intelligence test score.

That said, there is an active literature on practice effects. For example, see this question about practice effects on Raven's.

As a general principle practice effects are generally considered to be small on intelligence tests. The theory of skill transfer says that they will vary on a continuum based on the similarity between what has been practiced and what you are doing now. There also needs to be some capacity for domain-specific learning.

In your case, most free online tests that claim to be modelled on the Wonderlic or another commercial test are likely to be a very rough proxy.
More generally, the Wonderlic has a wide range of question types. Thus, I doubt that even taking an alternate form of the Wonderlic would make much difference to subsequent test taking efforts.
Also, when you do a test, you typically don't receive feedback on what is the correct answer. So, the capacity for incidental learning is limited.


Are there theories on how vocabularies for the Semantic Pointer Architecture are created?

I do not know for sure, but I believe that the vectors would be created in a domain-specific manner.  Vectors in the visual system would be created in a way that is particular to the needs of visual processing, etc.  The reason why the vectors are represented as random in the semantic pointer architecture, is because from the point of view of the architecture itself, the information encoded in the vector is irrelevant.  What is relevant is how to manipulate those concepts once they are already formed.


What does "The brain has its own language for testing the structure and consistency of the world." refer to?

Dr. Sagan is referring to the brain's ability to produce models of the world in order to test predictions.

In terms of psychology contemporary with Carl Sagan, he may have been referring to, in part, the theory of schemas. This is a general representation of a thing or idea that is used in classifying or identifying the thing or idea. In developmental psychology, the idea of Jean Piaget's schema might appear as a young child identifying all four-legged animals as "doggies." As the child grows, they will begin to differentiate, and for example, know horse vs. dog (but might classify a zebra as a horse).

The "language" of the brain seems to be an emergent property of neuronal firing. When a neuron elicits an action potential, it produces a voltage pulse that (usually) travels down the axon. Neurons can stimulate each other when synapses are triggered by an action potential of the pre-synaptic neuron. This is a simplified explanation: there are also graded synapses that aren't action potential-triggered.

Dr. Sagan might also have been thinking of the 1981 Nobel Prize-winning research by Hubel, Wiesel, and Sperry, whose mid-twentieth century research demonstrates how receptive fields for retinal neurons map onto the visual cortex. Retinotopic maps show how the brain putatively represents visual stimuli in the cortex.

In the early 1990s, researchers began investigating the "neural code" in earnest. A rate code is the idea that information is carried in the particular firing rate of a neuron, that is, the mean number of action potentials per second. A temporal code is when information is contained in the timing of spikes, not just the mean firing rate. Charles Frye has a great explanation with citations.

Symbolic processing in the brain is an active field of research. The problem can be approached from top-down neuropsychological assays, or from down-up electrophysiology. There is little doubt that symbolic processing is performed by neurons working in concert, though the exact mechanisms for all but the crudest processes are unknown.

Here are some examples: Theoretical models [1, 2] have shown how layers of neurons with different properties can be used to filter or transform data. In addition, high-level models have demonstrated possible methods by which cognitive units comprised of one or more neurons can determine the solution to symbolic problems [3]. In addition, electrophysiological assays show how cells in the cortex of mammals "record" and represent physical data for use in navigation [4].

[1] Gjorgjieva, Julijana & Drion, Guillaume & Marder, Eve. (2016). Computational Implications of Biophysical Diversity and Multiple Timescales in Neurons and Synapses for Circuit Performance. Current Opinion in Neurobiology. 37. 44-52. 10.1016/j.conb.2015.12.008.

[2] Shankar, K. H., and Howard, M. W. (2012). A scale-invariant internal representation of time, Neural Computation, 24, 134–193.

[3] Hasselmo ME, Stern CE (2018) A network model of behavioural performance in a rule learning task. Phil. Trans. R. Soc. B 373 : 20170275. PMCID: PMC5832697. PDF

[4] Hinman JR, Dannenberg H, Alexander A, Hasselmo ME. (2018) Neural mechanisms of navigation involving interactions of cortical and subcortical structures. J. Neurophysiol. 119(6):2007-2029. PDF


relation of substantive/verb to declarative/procedural memory

While it's true that universal nouns will link mostly to other universal nouns (a tree is a plant), and universal verbs will link mostly to other universal verbs (to climb is to move), it is not necessary that they be in separate memory areas from each other; or even that they be separate from event memory (one cat did climb one tree).  The most efficient memory scheme would minimize the length of all links.  One way would be to store all new memories in a fairly linear structure, and then use an off-line process (sleep) to spread them around to minimize total link lengths {or to optimize lengths around importance of fast access}.


How is the effect of current vote scores on people's votes interpreted in psychology?

I think you can find an answer from the field of social psychology. The most relevant theory is the social proof, the tendency to immitate the behavior of other people.

  Social proof (also known as informational social influence) is a
  psychological and social phenomenon where people assume the actions of
  others in an attempt to reflect correct behavior in a given situation.

  ...

  Social proof is one type of conformity. When a person is in a
  situation where they are unsure of the correct way to behave, they
  will often look to others for clues concerning the correct behavior.
  When "we conform because we believe that others' interpretation of an
  ambiguous situation is more accurate than ours and will help us choose
  an appropriate course of action", it is informational social
  influence.


Do highly creative people dream more and/or differently than ordinary people?

There are some studies that seem to support your suggestion e.g.:

Dream reports and creative tendencies in students of the arts, sciences, and engineering (paywalled, so I'm quoting the abstract):

  105 students of arts, sciences, and engineering were asked to report a dream and to take a test which measures independence of judgment and relates to creativity. 4 predictions were stated: (a) (confirmed)—the proportion of dream recallers would be greatest among art students and least among engineering students; (b) (partially confirmed)—dream imaginativeness would be greatest among art students and least among engineering students; [...]

Creativity and Dream Recall (same as above):

  The literature on creativity and dream recall often found significant positive correlations between measures of creativity and dream recall frequency (DRF). The present study investigated the relation between creative interests and DRF in detail. The findings confirmed the results reported in the literature, according to which persons with visual and verbal creative skills recalled more dreams. It is suggested that the visual memory may serve as a mediator variable in the relation between creativity and DRF.

Yet dream recall is a complex topic. As you noted in your comment, it might be different for a single person from night to night. It also seems to be inlfuenced by a lot of factors. Schredl et al. name some of them in Factors of home dream recall: a structural equation model:

Personality measures
Creativity/fantasy
Visual memory
Sleep behavior
Stress measures

Yet there are still a lot of factors more to be included, like demographic factors, attitude towards dreams, medication and so on (Schredl has written a lot about dream recall, if you want to dig deeper).

So I'd summarize creativity might increase dream recall but it's only a small part of a bigger picture.


What is the correlation between the development of the sense of self and the senses?

This question is quite broad, firstly, because these tests measure different (though interrelated) cognitive faculties and at different developmental stages and secondly because there is a lot to say for each sensory impairment. However, it touches on quite interesting topics for which there have been many studies and I think a summary of the findings can be made without being too big. For this purpose, it will be more useful to talk about the capacities that are associated with the tests rather than just studies with these tests, in order to get the bigger picture. Also , I would like to point that my answer is almost entirely about visual and auditory impairment because that is what I could find. If anyone knows of anything else, feel free to edit my post.

The Sally-Anne test is used by developmental psychologists to test the ability to attribute false belief which is a measure of one's theory of mind. Theory of mind is the "ability to attribute mental states — beliefs, intents, desires, pretending, knowledge, etc. — to oneself and others and to understand that others have beliefs, desires, and intentions that are different from one's own". As you described, this skill is almost fully developed at around 5 years of age.
The Mirror test or Rouge test (specifically for human infants) is used by develompental psychologists to test self recognition/self awareness which can be defined as "the ability to become aware of one’s own mental
and bodily states (e.g. perceptions, attitudes, opinions,
intentions to act) as one’s own mental and bodily states" (Vogeley & Fink, 2003). As you described infants pass this test around 18 months of age, however it has been suggested that self-awareness should not be viewed as a unitary achievement but rather as a process that has successive stages being fully developed at around 5 years of age (Rochat, 2003).

Both these tests have to do with the sense of self as distinct from other beings which according to the proposed developmental pattern that it follows is also not to be treated in a unitary fashion (for a review see Baumeister, 2010 and Geangu, 2008). Theory of mind is more associated with the aspect of self which is called interpersonal self while self recognition as measured by the mirror test is associated with what has been called as bodily self or body image (Geangu, 2008).

So referring to your question about the effect of sensory impairment to these abilities:

Regarding the theory of mind, there have been studies on blind and deaf children.Yagmurlu et al (2005) summarized such studies in their article.

  Research with deaf children has emphasized the role of environment, particularly exposure to
  conversation, in theory of mind development (Peterson & Siegal, 2000). In their review, Peterson and
  Siegal (2000) have shown that children’s access to conversation is correlated with theory of mind
  development. They found that profoundly deaf children with hearing parents who generally have almost
  no access to any communication means until they start school are more severely impaired in theory of
  mind development than orally trained deaf children who use hearing aids or deaf children with deaf
  parents who use sign language from an early age (Peterson & Siegal, 1998, 1999; Woolfe, Want, &
  Siegal, 2002) Further, Peterson and Siegal (2000) argue that early conversations, especially those about
  imaginary or abstract ideas, or about beliefs appear to be necessary cognitive input in theory of mind
  development.

  Research on children with visual impairment also shows that these children are delayed in theory of
  mind development (Green, Pring, & Swettenham, 2004; McAlpine & Moore, 1995; Minter, Hobson, &
  Bishop, 1998; Peterson, Peterson, & Webb, 2000). Visual impairment may limit communication with
  parents due to lack of shared visual experience (Minter et al, 1998), and may also impair understanding
  what is in others’ minds because access to visual cues is cut (Peterson et al., 2000). Despite this
  disadvantage, language skills of visually impaired children continue to improve, and their social
  experiences with peers and teachers become richer, which contribute to a gradual acquisition of theory of
  mind skills (Green et al., 2004)

Reviewing the findings of some of the above studies Malle (2002) suggested that anything that prevents the development of language and communication in general, is likely to cause a delay in the development of theory mind.

Regarding the mirror test, as it is dependent on visual cues alone, I don't think blind people would be able to pass it, while there is no reason to expect that people with hearing or olfactory impairment wouldn't pass it. Of course an inability to pass this test does not lead to the conclusion that blind people and especially congenitally blind people lack a sense of self and specifically a body image. This is likely achieved through different sensory inputs. Geangu (2008) noted that while a perceptual sense of self requires the integration of sensory information such as visual, auditory, tactile and kinesthetic, it is the proprioception and visual processing of the body that have  higher relevance for the construction of a personal representation of one’s body in space. Bermudez (1998) had a slightly different opinion.

  The developing child may first acquire
  a sense of self when it becomes able selectively to attend , in however ill
  differentiated a fashion , to its individual body parts in the somatosensory
  modality . It would then become acquainted with the internal causal consistency
  of their positions and displacements relative to its own volitions .
  The assumption that the visual channel soon reveals to the infant which
  body parts are its own (Neisser 1978) may be mistaken . Logically , the visual
  channel should soon betray which (body) parts are always present and
  one
  '
  s own and which (external ) objects are present only sometimes
  (Neisser 1978)
  . But the mechanisms for accomplishing this during development
  (Gibson 1969, Bower 1974) may follow rather than precede somatosensory
  attending . Poeck and Orgass (1964a, 1964b) found that blind
  children developed knowledge of their body at about the same age as
  sighted children

Also, maybe blind people can rely on auditory input from early age to form a sense of self and this view is supported by a recent imaging study (Ma & Han, 2011).

So, to conclude this section, while I didn't find enough empirical data on blindness or anything on deafness to support a typical development of self awareness in these people, I don't think there are enough reasons to think that such a developmental delay occurs when these sensory systems are impaired.


Bias of finding others guilty of own shortcomings

Your first paragraph, in particular, reminds me of the 'fundamental attribution error':

  ... the fundamental attribution error (FAE), also known as the
  correspondence bias or attribution effect, is the claim that in
  contrast to interpretations of their own behavior, people place undue
  emphasis on internal characteristics of the agent (character or
  intention), rather than external factors, in explaining other people's
  behavior.


What causes the sensation of taste when Dimethyl Sulfoxide (DMSO) is absorbed through the skin?

Short answer
It may not be so much the direct action of DMSO on the olfactory sensory system, but the smell of one of its metabolites that is excreted via the pulmonary system and the skin after ingestion of DMSO.

Background
Dimethyl sulfoxide (DMSO) is metabolized in man by oxidation to dimethyl sulfone (MSM) or by reduction to dimethyl sulfide (DMS) (Fig. 1).

Fig. 1. The reaction of DMSO to DMS catalyzed by DMSO reductase. source: wikipedia

DMS is eliminated through the breath and skin and is responsible for the characteristic garlic-like odor of the breath, and taste in the mouth associated with ingestion of DMSO. These effects can become noticeable minutes after ingestion and may last for several hours (Santos et al, 2003).

Reference
- Santos et al., Biochem Pharmacol (2003); 65: 1035-41


How did Fechner justify the assumption that the just-noticeable-difference in sensation is constant?

It was not an assumption; it was a decision. It allowed for better quantification, it gave an operational definition in increase in sensation, which allowed for more common ground in research between different labs. In a way, it's a definition by pure counting: when the subject feels a change in sensation, add one. Then this absolute scale is plotted against the ratio scale of increase in stimulation.


Is there any reason why chunking the digit span test would not help

As far as I know the effectiveness of chunking depends on (1) test speed and (2) amount of practice.

At low speed simple techniquest benefit almost everyone a little, even with virtually no practice. Quoting from Dempster and Zinkgraf

  Recently, in fact, evidence has been found that questions the validity of the assumption
  that chunking plays a role in digit-span variance. In one experiment,
  Lyon (1977) presented 12-item digit sequences to adult subjects for whom conventional
  digit-span estimates were available, and instructed them to think of each
  successive group of three digits as a three-digit number. The important result was
  that subjects with high spans (average = 8.3) benefited just as much from the chunking
  instructions as those with low spans (average = 6.1). Thus, prompting all subjects to
  impose a common structure on the lists did not produce the convergence of the two
  groups that would be expected if chunking was the source of differences between
  subjects in the high- and low-span groups.

On the other hand

  However, it does seem plausible that the temporal characteristics of
  the digit-span task (rapid presentation rate and single trial) simply allow little opportunity
  for chunking, unless the individual is exceptionally adept at creating
  chunks (Hunt & Love, 1972, pp. 248-250), or has received an extended period of
  practice (Ericsson, Chase, & Faloon, 1980; Gates & Taylor, 1925; Martin &
  Fernberger, 1929). For such an individual, chunking can be a highly successful
  strategy.

The "extended practice" mentioned there involves associative techniques not merely chunking.


What is the status of evolutionary psychology in academia today?

This is a bit of a quick answer and hopefully others will provide a more comprehensive response.

The number of reflexes that exist in humans is arguably a separate issue to the support for evolutionary psychology. The answer below focuses specifically on the support for evolutionary psychology in academic psychology.

Almost all researchers in psychology would agree that evolutionary processes have shaped what it means to be human. A good example of a well-developed theory is ACT-R, which provides a model of cognition. An underlying assumption of the theory is that the nature of the underlying structure of cognition has evolved to minimise the consumption of computational and biological resources (although you're better off reading ACT-R material directly to understand how they describe the interface of genetic and environmental adaptation, e.g., Anderson 1991). This still leaves many issues regarding how to conceptualise human nature and the extent of human plasticity.

However, "just so" arguments made in the name of evolutionary psychology are generally not respected in academic psychology. For example, Someone might say that women are better at multitasking because throughout evolution men's behaviour has required singularity of purpose in hunting and mate seeking, whereas women have had to juggle competing tasks of child rearing, looking after the camp, and so on. Of course, that's all rubbish. I just made that argument up out of nothing. Such an argument takes an observation, possibly not even true in the first place, and then seeks to find some vaguely plausible evolutionary story to justify it. It's a "just so" argument.
You can see further discussion of critiques of evolutionary psychology here.

References

Anderson, J. R. (1991). Is human cognition adaptive. Behavioral and Brain Sciences, 14(3), 471-517. PDF


What's the relation between BCM and Oja's learning rule?

Although the effects of BCM and Oja's learning rule have been explored superficially in a computational manner in the context of the NEF, judging from the results (which I've reproduced below) it isn't clear to me if they can/should be combined in any meaningful way.

The best hypothesis that I can come up with is BCM forces the ensemble to be either "ON" or "OFF" by minimising transitory states, while Oja provides limits to how much the connection weights can change. So in a way, Oja provides bounds to BCM? Further investigation is needed.


Do pictures help young children read (understand meaning) better or does it give them a delayed sense of imagination when decoding information?

I wrote Vexed Texts a long time ago. Since then I have asked the same question and found no research on it, so I did my own research as my doctoral thesis. You can find the results if you want to in my published thesis (I received my PhD from Victoria University in Wellington New Zealand). The title is: The Effect of Illustrations on the Ability of Children to Draw Inferences while reading Narrative Texts.


Why do we have so much neurological research on and treatment designed for dyslexia, yet less so for dyscalculia?

This website http://www.aboutdyscalculia.org/causes.html provides answers to some of the questions you posed, although I am not sure it is the most up to date information. I would always advise one to do research on more scientific grounds.
From my perspective, dyslexia has also been more studied than dyscalculia as its impact in academics seem more easily perceived thus easier to diagnose. Furthermore, I think that there is a social component to the issue as people often accept with ease someone struggling with mathematics but respond with more preoccupation towards difficulties with reading and spelling.
I leave you one article that may be helpful to you. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514770/


Introduction
It is interesting and quite under-researched topic in psychology. What has been studied and definied extensively are different abnormal sexual behaviours, and exhibitionism is one of them. In the DSM-IV exhibitionism is defined as sexual arousal by revealing one's body or performing sexual acts in public and it's a form of paraphilia. Attraction to being watched by others during  sexual intercourse is a form of exhibitionism called martymachlia. Presence of such sexual behaviours in DSM-IV is a clear indication that majority our society have deeply enrooted social and moral norms regarding inhibition sexual behaviour in public. If you think about it, majority of countries bans public sex and limits exhibitionism to designated places (nudist beaches and nudist colonies).
EDIT
Following valid and constructive comments by @Piotr and @Preece I removed speculative part of my answer about cultural factors and expanded my answer arguing for evolutionary explanation.
Territorial mating behaviour in animals
Initially I should point out that you are not exactly right in saying that 'most species don't practice private sex'. It's true that many primates do that. But we can argue that some territorial behaviours in animal kingdom are a form of providing security during mating. Those behaviours are very common in animal world including lizards (Davis, 1980), birds (Brown, 1969; Greenwood, 1980) and mammals (Greenwood, 1980).
Evolutionary development of shame
@PiotrMigdal specified that he is mainly interested in the issue of "unwillingness to have sex in public". We can trace the origin of such 'unwillingness' to the sense of shame that could be explained from evolutionary standpoint. Darwin (1872) argued that shame represents what would be at the primitive level an instinctive seeking for cover, but his elaboration on this wasn't clear. MacCurdy (1930) took this idea further. He argued that prehistoric man sought concealment for activities which expose him to danger in a hostile environment, e.g., eating, sleeping, sexual intercourse and excretion (Maccurdy, 1930). Concealment was sought prior to the fulfilment of any act that would limit or prevent rapid self-defence. For example, Maccurdy (1930) boldly pointed out that postures during both sexual intercourse and excretion prevents people from rapid self-defence.
Malinowski (1927) writes that:

it is characteristic that sexual activities, sleep and excretion are
surrounded by protective taboos and mechanisms of concealment and
isolation in almost every society.

In this context, the sense of shame could have developed as a response to natural drive for self-protection (Dawrin, 1872; Maccurdy, 1930). Therefore, evolutionarily this would form the basis of unwillingness of having sexual intercourse in public.
Because personal security increased with the development of civilisation, the sense of shame has also transformed and became more sophisticated (Maccurdy, 1930). The shame exists only for specific situations (e.g. public sex), but it doesn't apply in other social conditions. Maccurdy (1930) gives examples with excretion, where it isn't uncommon for partners to urinate in each others presence or in the presence of other friends. We can also put nudist beach in this 'shame-exclusion' category. Overall, evolutionary account would highlight that out need for private sex is related with growth for security, the extension of shame, and the evolution of modesty. Along the same line, Malinowski (1927) also points out that sexual intercourse in public could excite jealousy and would be an indicator to invite rivals to seize that which is being enjoyed.
References:

American Psychiatric Association. (2000). "Diagnostic and statistical
manual of mental  disorders" (4th ed., text rev.).
Davis, J. (1980) "The times of mating and oviposition of the Western
fence lizard S.o.occidentalis", J. Herpetol. 14:102
Brown, J. (1969) "Territorial behavior and population regulation in
birds: a review  and re-evaluation". Wilson Bull. 81:293-329.
Greenwood, P. J. (1980) "Mating systems, philopatry and dispersal in
birds and mammals."  Anim. Beha. 28, 1140-1162.
Darwin, C. (1872) "The Expression of the Emotions in Man and
Animals." London: John  Murray.
MacCurdy, J. (1930) "The Biological Significance of Blushing and
Shame." British Journal  of Psychology, 21, 174-182.
Malinowski, B. (1927) "Sex and Repression in Savage Society." London:
Kegan Paul, Trench,  Trubner & Co.


Any other studied psychological phenomena like reactance?

You may wish to look at Steindl, et al. (2015).
This paper presents an overview of research into Reactance that has been done since Miron and Brehm's 40 years review (2006) of all research since Brehm first proposed reactance theory (1966).
References
Brehm J. W. (1966). A theory of psychological reactance. New York, NY: Academic Press.
Miron A. M. & Brehm J. W. (2006). Reactance theory – 40 years later. Zeitschrift Für Sozialpsychologie/Journal of Social Psychology, 37(1), 9-18. https://doi.org/10.1024/0044-3514.37.1.9
Steindl, C., Jonas, E., Sittenthaler, S., Traut-Mattausch, E., & Greenberg, J. L. (2015). Understanding psychological reactance: New developments and findings. Zeitschrift fur Psychologie/Journal of Psychology, 223(4), 205-214.
https://doi.org/10.1027/2151-2604/a000222


Probably not. The closest thing I am aware of is Mayor et al (2016) [The Effect of Chronic Dieting Goals on Auditory Perceptual Biases] where they

  propose the existence of “wishful hearing,” which establishes that ambient product sounds can be perceived as more spatially proximal when more desirable and thus lead to increased purchase intentions and consumption.


Why do we need to know why something is needed or relevant?

The term I think of that is most associated with this concept is salience.
There is a massively informative world out there. If you were to spend all your time focusing your attention on arbitrary objects or sensations from the environment you would never get anywhere. You might die of starvation or some other unmet physiological need or get eaten by a tiger while focused on something that isn't dangerous and doesn't help you reproduce - this circumstance is not evolutionarily favorable.
Though salience is often focused on more immediate threats and benefits, more complex organisms including humans are able to plan ahead a bit and put effort into things now that have benefits in the future. Some things seem to be innately salient, others become salient with learning.


Cultural psychology: Japanese culture and meaning systems

First off - this question is really broad and its scope could probably fill libraries. I will therefore limit the answer to generalized pointers in answer to your three sub questions.

  Is there any place online where I can conduct an interview with Japanese people who reside in Japan and are familiar with their own culture.

Culture is a difficult concept. What I can say here is that every Japanese person is aware of their culture, because every Japanese is a part of their culture. Japanese culture is created by the Japanese inhabitants; it's what shapes them, it is the very air they breath. Conducting interviews is something that needs to be established and anthropologists often dive into the community of interest and spend considerable amounts of time to familiarize themselves with the culture, build a network and go from there. Understanding people, let alone their culture is not something that can be done easily from behind your computer screen I'm afraid.

  How can I identify actions, activities, and goals of the culture in order to construct a meaning system so as to understand and interpret the relationship between the actors (culture), tools (e.g., appraisal of the child's actions), activities, scripts, and goals?

The first step is to develop a specific research question and subsequently operationalize it. I am reading diverse questions and here's just an excerpt from your comments:

  ...pinpointing some activities and understanding some of their goals. [...] Why is the expression of negative emotions discouraged in a Japanese society? What do mothers do to cultivate their child's cognitive development? Do they encourage verbal communication, eye contact, exploration, etc... Do they breastfeed? How long and why that long? How do they discipline their child?

You seem to be struggling with a lot of questions lacking the necessary research focus. Especially an undergrad study should be meticulously defined and most of all restricted to make it operable in the short time window available.

  Do you have any tips on how to write an ethnography?

Libraries are filled on this topic. I can refer you to Clifford & Marcus, 1986.

Reference
- Clifford & Marcus, Writing Culture. The poetics and politics of ethnography. UC Press (1986)


How does the human brain store motor skills for long term?

I second the comments on the question that the question-post looks kind of convoluted. But it seems it all boils down to the question:

  How does our brain store motor skills without any apparent long-term potentiation or protein synthesis?

I personally think the question premise, i.e. "LTP and protein synthesis are not involved in motor learning", is incorrect to start with.

Firstly, motor learning has been linked to long-term potentiation in the primary motor cortex (Avinzino et al., 2015);
Secondly, protein expression is involved in motor learning as well. Fos expression has been used for decades as an immunohistochemical protein marker for neural activation. Fos expression in the motor cortex has been linked to motor learning, alongside synaptogenisis processes (Kleim et al., 1996).

References
- Avinzino et al., Front Behav Neurosci (2015); 9:105
- Kleim et al., J Neurosci (1996); 16(14): 4529-35


Why do the hemispheres of the brain control the opposite sides of the body?

The formal name for crossing in biology is decussation.  It is thought to be a result of anatomical development as well as a recovery mechanism.  Essentially, it's an emergent result of negotiations between genetics, development, and environment.  I've emphasized the relevant sentences in two abstracts below.

  Abstract: The crossing of nerve tracts from one hemisphere in the brain to the contralateral sense organ or limb is a common pattern throughout the CNS, which occurs at specialised bridging points called decussations or commissures. Evolutionary and teleological arguments suggest that midline crossing emerged in response to distinct physiological and anatomical constraints. Several genetic and developmental disorders involve crossing defects or mirror movements, including Kallmann's and Klippel-Feil syndrome, and further defects can also result from injury. Crossed pathways are also involved in recovery after CNS lesions and may allow for compensation for damaged areas. The development of decussation is under the control of a host of signalling molecules. Growing understanding of the molecular processes underlying the formation of these structures offers hope for new diagnostic and therapeutic interventions.

Vulliemoz, S., Raineteau, O., & Jabaudon, D. (2005). Reaching beyond the midline: why are human brains cross wired?. The Lancet Neurology, 4(2), 87-99.

  Abstract: Many vertebrate motor and sensory systems “decussate” or cross the midline to the opposite side of the body. The successful crossing of millions of axons during development requires a complex of tightly controlled regulatory processes. Because these processes have evolved in many distinct systems and organisms, it seems reasonable to presume that decussation confers a significant functional advantage—yet if this is so, the nature of this advantage is not understood. In this article, we examine constraints imposed by topology on the ways that a three-dimensional processor and environment can be wired together in a continuous, somatotopic, way. We show that as the number of wiring connections grows, decussated arrangements become overwhelmingly more robust against wiring errors than seemingly simpler same-sided wiring schemes. These results provide a predictive approach for understanding how 3D networks must be wired if they are to be robust, and therefore have implications both for future large-scale computational networks and for complex biomedical devices.

Shinbrot, T., & Young, W. (2008). Why decussate? Topological constraints on 3d wiring. The Anatomical Record, 291(10), 1278-1292.


What's the difference between stereotypes, prejudice and discrimination?

The terms are sometimes used a little differently. Nevertheless, in psychological research, there is quite some consensus about their use. For example, reflecting the most prevalent view, the Resolution on Prejudice, Stereotypes, and, Discrimination of the American Psychological Association (2006), defines them in the following way:

  prejudices are unfavorable affective reactions to or evaluations of groups and their members, stereotypes are generalized beliefs about groups and their members, interpersonal discrimination is differential treatment by individuals toward some groups and their members relative to other groups and their members, and institutional discrimination involves policies and contexts that create, enact, reify, and maintain inequality (Dovidio, Brigham, Johnson, & Gaertner, 1996; Eagly & Diekman, 2005; Fiske, 1998; Lott & Maluso, 1995; Mio, Barker-Hackett, & Tumambing, 2006; Myers, 2005; Nelson, 2005; Shih, Pittinsky, & Ambady,1999)

In other words, if Person A does not like (has a negative emotional reaction toward) the Lokai in general, or Person B (whether explicitly or implicitly) in particular because this person is a Lokai, that's prejudice.

If Person A believes that being a Lokai makes Person B a treacherous, lazy, and dumb guy, but a great cook and guitar player (you have to grant them that!) that's a stereotype.

If Person A doesn't invite Person B to his/her party because he/she is a Lokai, that's discrimination.


When I read a book I tend to read the words but to also hear them in my mind

Inner Speech is the general name given to this phenomenon,1  although it also goes by imagined speech, silent speech or covert speech, there are few studies and even less definite conclusions as to how it happens and its role in reading comprehension.

  and only after that I perceive the whole sentence.

In general, language comprehension goes through the perception of sounds, words and sentences followed by meaning ( independently or in succession) , in order to comprehend a sentence or paragraph you hold words or sentences in some form of short term memory, for visual language ( written words, sign language ), we have a visual sketchpad and for spoken words we have a phonological loop and other inter related memory structures,these buffers also connect or send information to other associational areas in the brain where meaning is presumably derived.2

  It seems to me that I can not control this process.

Another related concept to inner speech is private speech3, words spoken out loud to oneself. Private speech is both healthy and normal in children from the ages of 2 to 7 ( a student reading in class to himself in whispers for instance ), although we generally stop the public practice when we grow up due mostly to our social environment and other factors. It is then conceivable that our preferred way ( although not the only one) way of reading for comprehension is to use silent private speech which in turn goes through the language comprehension process outlined above.4

  My expectations are that reading has nothing to do with hearing.

Yes and no, while the entry point might be a different one ( visual vs auditory), most likely the language centers and higher associational areas get recruited by either one while reading or hearing, furthermore, by translating internally in between domains, you have access to memories specific to that domain, for instance: when perceiving visually a stop sign (and reacting rapidly), reading and imagining a color, or hearing how something smells5 .

  Any idea why this is happening?

Languages consisting of ideograms( Japanese kanji ) present some clues along with the previous overview. Even though the kanji ideograms have more in common with pictures than words; the principal speech comprehension centers get predominantly recruited ( there are still differences though).6 Language has also been predominantly spoken ( the written word is relatively new to our species ) so it makes sense from an adaptive perspective ( i.e it is more efficient) to have a language comprehension center devoted to the older spoken language ( or general sound deciphering) and co-opt it for reading, this new routing happens with the aid of inner silent speech ( which could be a modification of private speech) and other memory buffers.

Notes, reference & sources:

1. A great introduction and overview: Inner Speech: Development, Cognitive Functions, Phenomenology, and Neurobiology

2. Cognitive Neuroscience( Gazzinga) Has a great overview of language and memory and there are whole fields of Neurolinguistics and Psycholinguistics devoted to language.

3. The wiki on private speech and previous sources.

4. From Print to sound and meaning (Cognitive Neuroscience of Language -Kemmerer) presents a model of this arrangement.

5. A contrasting issue is early blind subjects that read in braile, the entry point here is tactile but ends up recruiting language and visual areas the same. see Visual Cortex Activity in Early and Late Blind People

6. Japanese and English sentence reading comprehension and writing systems: An fMRI study of first and second language effects on brain activation Presents a detailed account.


Revenge attitude: is it innate or acquired in human

Open access sources from Google Scholar:

Jackson, J. C., Choi, V. K., & Gelfand, M. J. (2019). Revenge: A multilevel review and synthesis. Annual Review of Psychology, 70, 319-345. https://doi.org/10.1146/annurev-psych-010418-103305

Lambert, A. J., Eadeh, F. R., & Hanson, E. J. (2019). Anger and its consequences for judgment and behavior: Recent developments in social and political psychology. Advances in Experimental Social Psychology, 60, 103-173.  https://psyarxiv.com/svcux/download?format=pdf


Our evaluation of the rationality of emotions depends on some social norm about the behavior and context of the behavior. On the other hand the somatic marker hypothesis states that there is logic in the inner workings of emotions. To illustrate somebody having an outburst while on his job may appear irrational to the public, even though there is rationality how this emotion was born.

The somatic marker hypothesis states that our decision making process is influenced by emotions (Damasio, 2000). Behavior that are associated with good outcomes are more likely to be repeated. Emotions and their bodily representations (somatic markers) serve as biasing signals for decision making. The case of Phineas Gage, a man that had an iron rod driven through his skull is used as example of not being able to use emotions in decision making, due to damage to the vmPFC.

According to the somatic marker hypothesis emotions and bodily changes(somatic markers) become associated with previous outcomes. This associations guide subsequent decision making processes. The markers can be activated through two distinct pathways. The first one is the body loop, where changes in the body are relayed to the brain. Being triggered by some sensory experience would fall into this pathway. The second pathway is as-if-body loop, where cognitive representations activate emotions. I think that the somatic marker hypothesis says emotions are embedded in our rationality rather than saying our emotions are rational.

To summarize I believe it is necessary to uncouple the evaluation of the rationality of some behavior and the processes guiding emotions.

References

Damasio, A. R. (2000). Descartes' error: Emotion, reason, and the human brain. New York: Quill.