# Question
Title: Does each sensory neuron type have a characteristic spike sequence pattern?
# Background

It is known that all sensory information is input to the brain as neural spike sequences. Now, to distinguish between the spike sequences generated by retinal red/blue/green cone cells from each other, and these from the cochlear (inner ear) hair cells, and so on, some sort of encoding scheme must be used.

To further clarify, in the case of retinal cone cells, the rate of incident light quanta in a given energy range, is the primary information that is coded. But, if all 3 types of cone cells generated identical responses for a given rate-of-incidence, like the CCD pixels in our digital cameras do, then there would be no way for upstream neurons to tell what type of cone cell a spike sequence came from. Instead, my guess is that, each type of cone cell encodes the rate-of-incidence in its own characteristic way, *similar to how different types of musical instruments sound differently, even when playing the same pitch at the same intensity, via timbre*.

An oversimplified illustration of Timbre

# Question

**Is there evidence that each sensory neuron type has a characteristic spike sequence pattern?**

# Why message type must be encoded in the message itself

During the development of the visual system, the retina, the LGN and the visual cortex develop separately initially and sometime later, axons from the retinal ganglions grow into LGN, and optic radiations from the LGN grow and reach into the cortex. *As far as we can tell* it is not guaranteed that a specific ganglion will project its axon to a specific neuron in the LGN. All that is guaranteed by the growth process is that ganglions close together will project to LGN neurons that are also close together.

Given this development process, when a higher region say in the V1 receives a spike stream from a neuron somewhere lower, the question arises: how does it know that this spike stream means, red, blue or green? A simple idea that occurred to me from information theory is that the message type could somehow be encoded in the message itself.

# Motivation

Evidence for characteristic spike patterns for each sensory neuron type would take us one more step towards understanding qualia, the hard problem of consciousness. ***My speculation is that qualia are the neuronal analogs of timbre in musical instruments.***

Erwin Schrödinger thought we'd never get there. He said, *"The sensation of color cannot be accounted for by the physicist's objective picture of light \[as\] waves \[or as quanta\]. Could the physiologist account for it, if he had fuller knowledge than he has of the processes in the retina and the nervous processes set up by them in the optical nerve bundles and in the brain? I do not think so."*

I guess he's right in the sense that we will never be able to fully wrap our minds around the mysterious and ineffable nature of qualia.

However, evidence of characteristic spike patterns would offer resolutions to qualia related thought experiments, such as Is there something about Mary?, that philosophers seem to be pulling their hair out over.

# Answer
This is an interesting idea, but I do not think it's correct. One piece of information that goes against the idea is this: auditory information is encoded by both frequency and amplitude modulation of neural spiking. The idea of spiking rate directly correlating with frequency is at odds with the idea of spiking rate containing this sort of "meta" information about the source of the activity.

We know quite a lot about how sensory information is represented in the nervous system. The simple fact of myelinated axons that don't interfere with each other already accounts for the problem you've proposed a solution for.

> if all 3 types of cone cells generated identical responses for a given rate-of-incidence... then there would be no way for upstream neurons to tell what type of cone cell a spike sequence came from

Here I believe is where you've made an error. The transmission of activity from the sensory neuron itself to an upstream neuron inherently conveys information about the sensation. The firing of the sensory neuron is a translation of the external phenomena to an internal neural code. No extra information is needed to represent the source of the activity.

**References**

Li Liang, L., Lu, T., & Wang, X. (2002) Neural Representations of Sinusoidal Amplitude and Frequency Modulations in the Primary Auditory Cortex of Awake Primates. *J. Neurophysiol* 87:2237-2261.
> 5 votes

# Answer
After an *eye opening* experience rereading Hubel's book, Eye, Brain & Vision and a bunch of papers, I found that the answer to my question is a superficial *yes* and a strong **no**.

It is unsurprising that neuroscientists have investigated if there are analog characteristics to neural spike streams:

> Neurons communicate with each other using stereotyped electric pulses, called spikes. It is believed that neurons convey no information other than the frequency of the transmitted spikes, called the firing rate. However, it is possible that neurons may communicate some information through the finer temporal patterns of the spikes because biological, as well as electrical/mechanical signals generally reveal internal conditions of the signal generator...
>
> ... First, we found that neurons exhibit stable firing patterns that can be characterized as “regular”, “random”, and “bursty”. Second, we observed a strong correlation between the type of signaling pattern exhibited by neurons in a given area and the function of that area.

So, in a superficial sense the answer is yes, sensory neurons might have characteristic firing patterns. However, when it comes to transmitting generic analog signals, neurons have one big handicap: ***any analog features in the signal are lost at synaptic junctions, where the electrical signal is transformed into a chemical message.***

One way to preserve at least part of the analog information, say message type encoded in a characteristic pattern, might be to have the message transmitted over *a sequence of neurons of the same size and type which all fire in a similar way*. However, in the visual system, there is no evidence for this. The retinal ganglion cells have their axons end in the LGN whose neurons are very different, and these in turn send their spikes to V1 whose neurons are again different. So, any characteristic patterns generated by the ganglions are lost in the LGN synapses.

The bigger question still remains: how do upper regions figure out what type of ganglion is sending the spike stream? (I'll formulate this more properly as a separate question).
> -2 votes

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Tags: neuroscience, consciousness, philosophy-of-mind
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# Question
Title: What is the role of traveling waves in circuit formation during cortical development?
Propagating waves of activity have been characterized in various regions of the brain such as the visual cortex (Nauhaus et al., 2012). Recently they have been reported for the first time to occur transiently during the developing cerebellum (Watt et al., 2009).

I'm curious as to how they would be important during early development and why they are transient which I'm sure the authors have moved on to try and answer as well.

I've heard before about neuronal activity being important for pruning and forming correct connectivity within a network. For example waves of activity has been shown to be required for the development of precise retinotopic maps (Chang et al., 2005).

I'm not an expert and not familiar with the history or literature of neurodevelopment, so would like to ask if someone who may be more knowledgeable to describe what's known about wave activity during early brain development in other brain areas. How do waves help with proper circuit formation in these other regions? I am hoping this might provide insight to its role in the cerebellum.

<sub> Nauhaus, I., Busse, L., Ringach, D. L., and Carandini, M. (2012). Robustness of traveling waves in ongoing activity of visual cortex. The Journal of Neuroscience, 32(9):3088–3094. doi:10.1523/JNEUROSCI.5827-11.2012
Watt, A. J., Cuntz, H., Mori, M., Nusser, Z., Sjöström, P. J., and Häusser, M. (2009). Traveling waves in developing cerebellar cortex mediated by asymmetrical purkinje cell connectivity. Nature neuroscience, 12(4):463–473. doi:10.1038/nn.2285
Cang, J., Renterı́a, R. C., Kaneko, M., Liu, X., Copenhagen, D. R., and Stryker, M. P. (2005). Development of precise maps in visual cortex requires patterned spontaneous activity in the retina. Neuron, 48(5):797–809. doi:10.1016/j.neuron.2005.09.015 </sub>

# Answer
Traveling waves are a developmental mechanism to "prime" neural circuits. In a mature adult, certain mechanisms allow the strengthening and weakening of synapses (LTP/LTP, dendritic spine growth, etc...). These same mechanisms are used during development to achieve initial connectivity. For these to work however, spiking activity must be present. Experience will later produce complex and meaningful patterns of activity between structures, that will in turn produce complex and meaningful patterns of connectivity. Until that point, the neural structures must be synaptically linked so that learning can begin after birth.

Certain cellular mechanisms guide axon growth, and this transient bursting activity "captures" the specificity of these growths as synapses. When this bursting activity is disrupted, the precise topographical connections are lost.

**References**

http://www.sciencedirect.com/science/article/pii/0896627393901228 http://www.annualreviews.org/doi/abs/10.1146/annurev.neuro.28.061604.135714?journalCode=neuro
> 4 votes

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Tags: neuroscience, developmental-psychology, neural-network, theoretical-neuroscience
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# Question
Title: Reducing adverse impact, discrimination and unfairness when using psychological assessments for selection purposes
How can we reduce adverse impacts such as bias, discrimination, and unfairness when using cognitive ability tests and personality tests for selection purposes in an international context?

# Answer
> 4 votes
*This is a big and important topic. The following is a bit of an introduction. Feel free to ask a separate more focussed question.*

### Some terminology

In general distinctions are made between the terms bias, fairness, and discrimination.

* **Bias** is a statistical term. Bias for a group can indicate that test scores for that group are systematically lower or higher than would be expected from the group's true score. It is often assessed by seeing whether there is a group by test interaction in predicting the criterion. In particular, just because groups differ in means does not mean the test is biased, the groups may differ on the underlying construct.
* **Fairness** is a moral and ethical construct. There is scope for different people to value different things. For example, using a test that while unbiased , reduces the prevalence of a minority group, may still be seen as unfair. Likewise, affirmative action might be seen as fair in the context of a history of discrimination, yet others may perceive that is being unfair to the non-minority group.
* **Discrimination** is often used in a legal sense to refer to either direct or indirect forms of discrimination.

### Reviewing this area

I strongly recommend you read page 16.16 onwards (from the section labelled "Improved understanding of subgroup differences") of Sackett and Lieven's (2008, PDF) review.

In particular they note that several good predictors of task performance also show subgroup differences. Thus, there is sometimes a trade-off between validity and adverse impact. For a review of subgroup differences see Hough et al, 2001.

I quote a few sections with particular relevance to the question of what can be done to minimise adverse impact:

> Sackett et al. (2001) reviewed the cumulative evidence and concluded that several proposed mechanisms are not, in fact, effective in reducing differences. These include (a) using differential item functioning analysis to identify and remove items functioning differently by subgroup, (b) providing coaching programs (these may improve scores for all, but group differences remain), (c) providing more generous time limits (which appears to increase group differences, and (d ) altering test taking motivation.
>
> Sackett et al. (2001) did report **some support for expanding the criterion as a means of reducing subgroup differences**. The relative weight given to task, citizenship, and counterproductive behavior in forming a composite criterion affects the weight given to cognitive predictors. Sackett et al. cautioned against differential weighting of criteria solely as a means of inﬂuencing predictor subgroup differences; rather, they argued that criterion weights should reﬂect the relative emphasis the organization concludes is appropriate given its business strategy. They also reported some support for expanding the range of predictors used. The strategy of supplementing existing cognitive predictors with additional predictors outside the cognitive domain can reduce the overall subgroup differences in some circumstances. This strategy has received considerable attention because broadening the range of predictors has the potential to both reduce subgroup differences and increase validity

### International context

If you're particularly interested in the international context check out Myors et al (2008) which provides an overview of the context of selection and adverse impact from the perspective of a wide range of different countries.

### General thoughts

In general, there is also a wide range of general strategies that we might recommend to increase fairness. e.g., Ensure that choice of selection tools is based on a thorough job analysis and an understanding of the competencies required for the job; Use well-validated measures; standardise decision making processes; minimise potential for cheating; etc.

### References

* Hough LM, Oswald FL, Ployhart RE. (2001). Determinants, detection and amelioration of adverse impact in personnel selection procedures: issues, evidence and lessons learned. International Journal Selection & Assessment. 9:152–94.
* Myors, B., Lievens, F., Schollaert, E., Van Hoye, G., Cronshaw, S.F., Mladinic, A., Rodr\\'\iguez, V., Aguinis, H., Steiner, D.D., Rolland, F. & others (2008). International perspectives on the legal environment for selection. Industrial and Organizational Psychology, 1, 206-246. PDF
* Sackett PR, Devore CJ. 2001. Counterproductive behaviors at work. See Anderson et al. 2001, pp. 145–64
* Sackett, P.R. & Lievens, F. (2008). Personnel selection. Annu. Rev. Psychol., 59, 419-450. PDF

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Tags: io-psychology, measurement, selection-recruitment
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# Question
Title: Is there an effect of visual expertise on eye movements when examining an image?
In the following linked image, you can see the eye movement traces of a subject examining a bust of Nefertiti (I came across this image while reading the following blog).

When I was in grade school, I often heard art teachers claim that they were "not teaching us to draw or paint or sculpt... but teaching us to SEE". From personal experience with human figure drawing, it appears to me that the most observable change that comes with practice in drawing the human form from observation is learning to pay attention to the most essential details.

**My question:** Is there any reason to believe that if we were to take a group of people who could be considered to have "visual expertise" (let's say they have years of experience with observational drawing), that we would find notable differences in the patterns of their eye movement traces when scanning an object such as the Nefertiti bust shown above... when compared with people who do not have such expertise?

If you believe that we would observe such a difference... what evidence and/or theory leads you to believe this? Otherwise, what evidence and/or theory leads you to believe that it would be unlikely to observe such a difference?

# Answer
> 8 votes
There is a substantial literature on eye tracking.

### Skill acquisition example

One study that I am familiar with and is of some relevance is Study 2 in Lee and Anderson (2000, PDF). Specifically the study used eye tracking tools to examine how visual attention was allocated over time on an air traffic control simulator. The broad finding, consistent with skill acquisition theory was that:

> Overall, as people become more skilled, they appear to be reducing the time they ﬁxate on all the task-irrelevant regions while maintaining the amount of time spent on the task-relevant regions in the move unit-task. (p.305)

Thus, this study shows that at least on a task, as you would expect visual attention changes as a function of the development of expertise.

### A specific study of eye movements comparing experts and novices

It seems obvious that when visually examining art, people differ in how they view it. It also seems plausible that experts viewing art may focus on different things to novices. After a little searching I found a study by Vogt and Magnussen (2007) that appears to directly address your interest:

> In two sessions with free scanning and memory instructions, eye-movement patterns from nine artists were compared with those of nine artistically untrained participants viewing 16 pictures representing a selection of categories from ordinary scenes to abstraction: 12 pictures were made to accommodate an object-oriented viewing mode (selection of recognisable objects), and a pictorial viewing mode (selection of more structural features), and 4 were abstract. **The artistically untrained participants showed preference for viewing human features and objects, while the artists spent more scanning time on structural/abstract features.** A group by session interaction showed a change of viewing strategy in the artists, who viewed more objects and human features in the memory task session. A verbal test of recall memory showed no overall difference in the number of pictures remembered, but the number of correctly remembered pictorial features was significantly higher for artists than for the artistically untrained viewers, irrespective of picture type. No differences in fixation frequencies/durations were found between groups across sessions, but a significant task-dependent-group by session interaction of fixation frequency/duration showed that the artistically untrained participants demonstrated repetition effects in fewer, longer fixations with repeated viewing, while the opposite pattern obtained for the artists.

They also summarise existing research (see the article for more information):

> Picture perception in artists and laymen has been compared in several studies on the assumption that artists view the world differently from others. ... In one 12-s recording session, Nodine et al (1993) found that artistically untrained viewers tended to spend more time viewing individual objects than relationships among elements in paintings... Other authors have reported different eye-fixation patterns in artists and non-artists viewing pictures. Antes and Kristjanson (1991) found that eye-movement parameters alone could differentiate artists from non-artists by fixation densities on less important aspects of paintings, with 'important' being defined a priori by one professional artist (rather than by the experimenters according to hypotheses). Zangemeister et al (1995) found that artists and sophisticated viewers used a more global scanning strategy than artistically untrained participants when viewing abstract pictures.

### References

* Antes J R, Kristjanson A F, 1991. Discriminating artists from nonartists by their eye movement patterns. Perceptual and Motor Skills 73 893 ^ 894
* Lee, F.J. & Anderson, J.R. (2001). Does learning a complex task have to be complex?: A study in learning decomposition. Cognitive psychology, 42, 267-316. PDF
* Nodine F, Locher P J, Krupinski E A, 1993. The role of formal art training on perception and aesthetic judgement of art compositions. Leonardo 26 219 ^ 227
* Vogt, S. & Magnussen, S. (2007). Expertise in pictorial perception: eye-movement patterns and visual memory in artists and laymen. PERCEPTION-LONDON-, 36, 91. PDF
* Zangemeister W H, Sherman K, Stark L, 1995 Evidence for a global scanpath strategy in viewing abstract compared to realistic images. Neuropsychologia 33 1009 ^ 1025

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Tags: reference-request, perception, vision, sensation, expertise
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# Question
Title: What causes gender differences in responses to farting?
**Background:** By casual observation, I have noticed that males tend to react differently to the sound of a fart. It seems that men are more likely to laugh whereas women are more likely to show signs of disgust. I thought that perhaps there might be some evolutionary basis for this.

### Questions

* Is there any serious psychological research on the causes of our responses to farting?
* Are there any systematic gender differences?
* What are the posited causes of such gender differences?

# Answer
> 9 votes
I was shocked at how difficult it was to find systematic scientific research on the psychology of flatulence. The main empirical paper appears to be one by Lippman (1980). It seems to be hard to get a copy of the original. However, the author of the Neurotic Physiology blog discusses the paper at length.

### Lippman study

Lippman asked participants to rank various hypothetical farters based on various factors. With regards to sex differences the blogger writes:

> The sex differences were a little surprising. It turns out that women are more forgiving of loud, accidental farts (girls, we've all been there I'm sure), and don't ding the farter so much on "politeness"

However, when you think about the problem there are different kinds of sex differences in fart ratings: Men rating male farters; men rating female farters; women rating male farters; and women rating female farters. This question really only addresses how women rate others in general.

### Toilet psychology

Recently, a book was released by Professor Nick Haslam called "Psychology in the Bathroom". There's a good summary in The Psychologist (2012, PDF). The book specifically aims to redress the lack of psychological research devoted to excretion and related matters.

One particular passage from the book summary in *The Psychologist* may provide a potential explanation for gender differences in perceptions of farting:

> A common thread running through these differences is that **women’s excretion is more hidden, emotionally fraught and suppressed than men’s**. The incompatibility of femininity and excretion is nicely expressed in Jonathan Swift’s poem ‘The lady’s dressing room’, in which a suitor sneaks into his beloved’s room only to find evidence of her dirty corporeality, including sweaty garments, beslimed towels and encrusted combs. Upon discovering her chamber-pot he slinks away in horror, lamenting ‘Oh! Celia, Celia, Celia shits!’ The same sentiment is expressed less poetically by an American undergraduate: ‘women are supposed to be non-poopers’ (Weinberg & Williams, 2005, p.327). Despite our enlightened modern attitudes to gender equality, women are still judged more severely for violations of this ideal of untaintedness than men. In one study (Goldenberg & Roberts, 2004), a female experimenter who excused herself to use the bathroom was evaluated more negatively than one who excused herself to get some paperwork: no such difference was found for a male experimenter.

### General thoughts

So in summary, research on farting has generally been neglected by the psychological literature.

There is some evidence to suggest that women who fart are judged more negatively than men who fart. However, presumably this would vary a lot with context, who is farting, and who is recognising the farting. It would also presumably be a cultural phenomena.

One theory to explain gender differences is that a lack of purity is often associated with activities related to excreting, such as farting. Farting loudly or openly may symbolise a lack of control over excretion or remind others that a person is an excreting being. Purity is sometimes associated with a feminine ideal. Thus, farting may be socially more detrimental for a female than a male. Anyway, the preceding statements are largely based on theory; I'd like to see a lot more empirical evidence before I take them too seriously.

### References

* Lippman, LG. "Toward a social psychology of flatulence: The interpersonal regulation of natural gas". Psychology: a Quarterly Journal of Human Behavior, 1980.
* Goldenberg, J.L. & Roberts, T. (2004). The beast within the beauty: An existential perspective on the objectification and condemnation of women. In J. Greenberg, S.L. Koole & T. Pyszczynski (Eds.) Handbook of experimental existential psychology (pp.71–85). New York: Guilford.
* Haslam, N. (2012). Psychology in the Bathroom. Palgrave Macmillan.
* Haslam, N. (2012), Toilet psychology. The Psychologist. 25, 6, 430-433. PDF

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Tags: evolution, sex-differences, physiology
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title: Hebbian Learning Rule, Local or Global?

text:
# Question
Title: Hebbian Learning Rule, Local or Global?
I just learned about the Hebbian Learning Rule. It essentially says "Neurons that fire together, wire together". I'm wondering if the learning rule is affected by the spatial distance of the two neurons. When two neurons are far from each other, why is the connection formed?

# Answer
It's a local rule. All that it means is that the connection between two neurons gets stronger if you use that specific connection more. The specific connection (the synapse) must be used though; it doesn't apply to two random neurons that aren't connected that happen to fire at the same time.

Hebbian learning is generic term for outcome; there are actually two separate mechanisms I know about (probably many more, too). First, there's "silent synapses" which have only NMDA receptors, but not AMPA receptors. NMDA receptors have Mg+ molecules blocking their channels and require AMPA activation to expel the NMDA. So if you have a synapse with no AMPA, it won't be an effective synapse. However, if you have another synapse activing the tissue, expelling the magnesium, then the silent synapse has a short window to activate the synapse during the Mg expulsion. As it does this, it activates a series of protein signaling and transcription signaling that tells the cell to bring more AMPA up (a response to all the Ca signaling that these signals rely on). This is also a mechanism for conditioning (the two different synapses representing the pathway of the conditioned and the unconditioned response. The conditioned response would be the pathway with the silent synapse).

Another example is astrocytic regulation of glutamate levels. ATP is what your whole body uses for energy, but there are ATP detectors in astroctyes, which couple in the tripartite synapse as a synaptic regulator. As the synapse is more active, ATP is released, which activates the astrocyte and causes it to release extra glutamate, bringing the postsynaptic neuron closer to firing.

All of these require only that the neurons make contact at a synapse, distance between somas is not a factor. Of course, the distance between the axon and the dendritic spine have to be close enough to form a synapse.
> 12 votes

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Tags: neuroscience, learning, neural-network, theoretical-neuroscience
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# Question
Title: Web-based tools for documenting studies?
I am interested in how open science could be done in psychology. Are there good web-based tools that could house and share a study? When I say "study" I mean:

* Lab notes from collecting data
* Raw data
* Code for analyses
* Results
* Discussion of research process and results (ideally open to the community)
* Posters, Presentations, Publications

Right now all I have seen done (and my best idea) would be a combination of a Wiki for the lab notebook, cloud storage (e.g., Google drive) for the data, github (or similar) for the code, blogs for discussion, and a personal website for archived versions of journal articles, posters, and presentations.

# Answer
> 7 votes
The Open Science Framework will do some of what you ask for. Additionally, it will **allow** you to preregister your hypotheses to properly distinguish confirmatory and exploratory research.

## Features (quoted from the homepage).

> * Document and archive studies
> * Share and find materials, scripts, data
> * Detail individual contributions
> * Increase transparency
> * Time-stamp materials

# Answer
> 5 votes
I like your question. But I have to point out one thing - if you were to use documenting tools for all those tasks that you mentioned, you wouldn't have that much time left for your research. Sharing is great, but it takes time to do it properly, even with great tools.

I tried quite a few tools for documenting research, with an idea to boost my productivity, increase amount of recorded information and share the information for peers criticism. At the end of the day, only a tiny handful of those tools survived. The ones that survived were the ones that smoothly integrated with my daily routine, mainly in terms of time efficiency and interface simplicity.

For the lab notes, quick thoughts, brutal sketches, small brainstorms and rapid conference scribbles, the winner is a **good quality paper notebook**. I am personally a fan of Paperchase A5 brown recycled paper jorunal with wiro bound, which I always use with thin black ink Pilot pen. I know, OCD, but in a good way. Brown paper gives this vintage quality to my notes, which is somehow stimulating for me, and I like to come back to it and store it. I tried alternatives, but they could never beat brown paper wiro bound. Livescribe pen was too big, with ugly ink, and lacking smoothness of software exporting and it ended up being only a voice recorder, rarely tho. iPad note taking apps like Noteshelf or Penultimate with Pogo stylus really slowed me down, ugly writing again, and the battery always died in the middle of important seminar.

I frequently make a snapshots of my paper notebook with Evernote using iPhone. I actually make a snapshots of many other things using **Evernote** and this is definitely very simple and great storage/sharing platform, that works smoothly between desktop and mobile.

For the raw data - Dropbox. Now, also Google Drive, as you pointed, but **Dropbox** was first, with cloud-based, super-simple set-up storage solution. Dropbox was a big thing in my documenting toolbox as it removed the need for USB dongles. I could set up my experiment to save all the participant's raw data automatically in Dropbox after the experiment. I came back home - it was there waiting for me. When we collaborated, all the data was nicely shared in collective Dropbox folders without the need to shuffle e-mails or set up transfers with raw data.

Mendeley is a great tool for both bibliography management and sharing. Fantastic idea that turned out really big and beats the shit out of EndNote. Major thing I love in **Mendeley** is the ability to automate creation of bibliographies for LaTeX. This is an ultimate time saver.

Regarding posters there is this new poster repository F1000 which I haven't tried, but it looks promising.

For analysis code I found it tricky. Yes, you can put code in Github, but you can't compile it there. So there is this extra step when you have to organize your code on Github, describe it, etc. Never tried it because I prefer to spend time to learn more coding, but I don't say I won't try it in the future, when I will feel I have more valuable code to share with community.

For presentation I played with Prezi for some time which has a cool option to share your presentations easily. But ultimately I abandoned it, after people complained about motion sickness and after I felt I lost some key simplicity factor. I am having my eye on Beamer but there is no time now, so Keynote has to suffice.

Regarding discussion, chat, intelligent monologue - again it depends on what you want to achieve with it. Share a coding trick in analyzing some data? Discuss some exciting data? Or write a page about your documenting toolbox approaches? In all cases it requires time, so it's good to make sure that you don't do it to avoid doing something more important. Tools for online discussion and blogging are numerous. I like it here in Stack Exchange, because it's purely community driven and it's very easy to put together an overlong piece of rant on many many topics ;-)

# Answer
> 4 votes
Figshare is one option for archiving assorted research artefacts. To quote the "about page":

> figshare allows researchers to publish all of their research outputs in seconds in an easily citable, sharable and discoverable manner. All file formats can be published, including videos and datasets that are often demoted to the supplemental materials section in current publishing models. By opening up the peer review process, researchers can easily publish null results, avoiding the file drawer effect and helping to make scientific research more efficient. figshare uses creative commons licensing to allow frictionless sharing of research data whilst allowing users to maintain their ownership. figshare gives users unlimited public space and 1GB of private storage space for free.

A few things that I like about figshare:

* Creative commons licence
* They have some form of archive policy which says that if they go out of business, the content will be backed up by another provider. However, it's not quite as open as stack exchange in that they don't make public backups of the entire site available.
* Objects get a citable doi
* View and share statistics for shared objects

# Answer
> 2 votes
The site http://psychfiledrawer.org/ also addresses some aspects of what you are asking. It is mainly geared toward maintaining a public repository of replication attempts of psych experiments.

# Answer
> 1 votes
A lot of labs I know use Basecamp. It *does* cost money, but provides a centralized place to store all the information you listed and allows for comments on all of it, as well as a calendar to coordinate your team.

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Tags: methodology, reproducible-research, internet
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# Question
Title: Judgments of similarity between samples of writing
I was thinking last night about the possibility of an experiment that investigates the factors contributing to peoples' judgments of 'stylistic similarity' between two samples of writing. For example, such an experiment might consist of multiple trials for each subject, each of which would present a different set of say 3 short excerpts of writing (text randomly sampled from a corpus of authors' writings... maybe no more than 500 words each). Each participant would be asked to make a judgment of either "Which 2 of these writings are most similar in style?" OR 'Which 2 of these writings were most likely created by the same person?".

Part of the data analysis and interpretation might involve the use of programs similar to this one: http://www.hackerfactor.com/GenderGuesser.php . Researchers could form hypotheses about relatively low-level factors that might be important in peoples' judgments of stylistic similarity, and then write programs that would make judgments based on these low-level factors.

I'm assuming that research resembling or even perfectly matching what I've described above has been conducted in the past. After reading what I've written above, does anyone have any suggestions for relevant readings?

# Answer
> 1 votes
It sounds like you're talking about Latent Semantic Analysis. Here's their rundown of what it is.

> However, LSA as currently practiced has some additional limitations. It makes no use of word order, thus of syntactic relations or logic, or of morphology. Remarkably, it manages to extract correct reflections of passage and word meanings quite well without these aids, but it must still be suspected of incompleteness or likely error on some occasions.

It's used in a lot of automated grading programs, or systems designed to give a score to paper based on some criteria. However, because order doesn't matter, it makes syntactic and grammatical coherence much harder to measure, so quantifying 'style' might be a little hard, unless by 'style' you mean something like word choice, phrase choice, etc.

Here's a gscholar search. The first three should give a good overview.

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Tags: reference-request, cognitive-modeling, computational-modeling, linguistics, reading
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# Question
Title: Problem understanding the calculation of normative (Bayesian) base rates
I am having trouble understanding Table 1 of Gigerenzer, Hell, and Blank (1988, PDF, table on page 516):

Focusing on the Jack row, it is stated that the mean probabilities of Jack being an engineer were 71.4% in a low base rate condition and 81.3% in a high base rate condition. Thus participants partially took base rates into account. If they were completely ignoring base rates these values would be the same, rather than being separated by 9.9%. So I believe I understand what is going on in the Base Rate Neglect column.

However, I don't understand what is going on in the Bayesian column. There is an explanatory footnote on p516 but to me it was not illuminating. The footnote provides the following equations:

$$p\_{70}(E|D)/(1-p\_{70}(E|D)) = L\frac{0.7}{0.3}$$ $$p\_{30}(E|D)/(1-p\_{30}(E|D)) = L \frac{0.3}{0.7}$$

So, since the mean guess for the 70% condition was 81.3% we get

$$ \begin{align} 81.3/18.7 & = L ~ 0.7/0.3 & \\ & = 81.3/18.7 & = L ~2.33 \\ & = 4.35 &= L ~2.33 \\ & = 1.86 &= L \\ \end{align} $$

However, then when I plug this $L$ value into the $p\_{30}$ equation I get a value for $p\_{30}(E|D)$ that deviates wildly both from the 'Bayesian' value and from what was actually observed. According to the table the average deviation from the Bayesian should be 16.1%, but according to my calculations it is much higher. It would be greatly appreciated if someone could tell me what I am doing wrong.

### References

* Gigerenzer, G., Hell, W. & Blank, H. (1988). Presentation and content: The use of base rates as a continuous variable.. Journal of Experimental Psychology: Human Perception and Performance, 14, 513. PDF

# Answer
I think you are doing the computation correctly, but Gigerenzer and Blank did not provide us with the full results of their experiment, preventing us from repeating their computations exactly: The data provided in columns 1 and 2 of the table are only the **averages**. The data in column 4 (Bayesian) is not a transformation of the average value using some formula (see below), but **the original data transformed, and then averaged**:

> For each subject in the 70% base rate group we predicted, by using Bayes's theorem, how this subject would have responded in the 30% base rate group

If you divide the first equation of the footnote by the second, and derive a formula for p30 as a function of p70, you get:

$$p\_{30}(E|D) \approx \frac{p\_{70}(E|D)}{5.44-4.44p\_{70}(E|D)}$$

Notice that this function is strictly convex in the region \[0,1\], meaning that if you compute it on the average p70, you'll get a value that is lower than the value you would get by averaging the values for several data-points.

As an example, lets examine the Jack row: If you transform the mean p70 of 0.813, you get p30 of 0.44, which has a deviation of 0.27 from the observed mean p30 (as you probably found). Let's assume that the data in the Jack row, in the p70 column was obtained from two subjects, that responded 0.968 and 0.658 (yielding the average 0.813 that is reported in the table). Transform both of these values, and you'll get 0.848 and 0.261, respectively, yielding an average p30 of 0.553, which would give a Bayesian deviation of 0.161 exactly as reported in column 4.
> 5 votes

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Tags: cognitive-psychology, decision-making, bayesian
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# Question
Title: What is a source of case studies of personality disorders?
**What is a good source for case studies on a broad range of personality disorders?**

I'm a writer and I'm interested in reading some case studies for character work. I've found some websites with classic case studies, but I would really like to find some something less historical, more modern.

Everything I've found online so far is topic related or deals with research studies that put people in tests (like the Stanford Prison Experiment).

Something like Clinical Case Studies would be great, but the articles are about $30 bucks online. **Are there any open-access journals or website with articles like Clinical Case Studies?**

# Answer
> 4 votes
Clinical Case Studies is a journal devoted to the write up of case studies. To quote the site:

> It presents cases involving individual, couples, and family therapy. The easy-to-follow case presentation format allows you to learn how interesting and challenging cases were assessed and conceptualized, and how treatment followed such conceptualization. This practical format allows clinicians to replicate successful treatments in their own practices.

Articles follow a 12 step format:

> 1. Theoretical and Research Basis for Treatment
> 2. Case Introduction
> 3. Presenting Complaints
> 4. History
> 5. Assessment
> 6. Case Conceptualization (this is where the clinician’s thinking and treatment selection come to the forefront)
> 7. Course of Treatment and Assessment of Progress
> 8. Complicating Factors (including medical management)
> 9. Access and Barriers to Care
> 10. Follow-Up (how and how long)
> 11. Treatment Implications of the Case
> 12. Recommendations to Clinicians and Students.

You can search within the publication using Google Scholar (publication = clinical case studies).

If price per article is an issue, a few options include:

* get access through a library or university.
* Subscribe to the entire journal ( this is generally cheaper than per article costs).
* examine the subset of articles where authors provide a copy of the PDF online. In Google scholar, see the articles with **\[PDF\]** in brackets.

### Example article

E.g., See this example by Leedy, Jackson, and Callahan (2007):

> The following case study illustrates a client-centered, cognitive-behavioral approach to the psychological treatment of Mr. M, a 41-year-old male diagnosed with chronic Lyme disease, a mood disorder from Lyme disease, and narcissistic personality disorder. Mr. M’s personality difficulties are conceptualized as representing compensatory narcissism, a strategic way of coping with feelings of insecurity. The goals of treatment included positively integrating Mr. M’s chronic illness into his identity, decreasing depressive symptoms, and improving his interpersonal skills. Treatment was successful in decreasing both Mr. M’s depressive symptoms and his narcissistic orientation to thinking and interacting with others.

### References

* Leedy, M.J., Jackson, M. & Callahan, J.L. (2007). Treating Depression and Compensatory Narcissistic Personality Style in a Man With Chronic Lyme Disease. Clinical Case Studies, 6, 430-442. PDF

# Answer
> 2 votes
Not sure if this is what you're looking for, but here are a few major academic journals on neuropsychology and neurology (in no particular order):

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Tags: reference-request, abnormal-psychology
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# Question
Title: Does writing something down help memorize it?
This is a question inspired by this recent question on the Chinese Language & Usage website.

Someone asked why they needed to learn how to write Chinese characters, since today we mostly use computers or text messages to do so. Several users replied that writing Chinese characters help remembering them more easily, including for reading purposes.

However, another user argued that there was no reason to believe that it was true, and that writing characters doesn't necessarily help one remember them (compared for example to simply reading them and looking at them).

Is that the case? Does writing generally help remember glyphs (or more generally information) or not? Is there any conclusive research about this or about the relation between writing and memorizing in general?

# Answer
Yes, writing increases the modality and attention given to a piece of information. Increasing the effort and the ways that you have experienced a bit of information helps you encode that information better; this is Elaborative Encoding.

More generally the more *deeply you process* a thing the more likely you are to properly encode the memory for future retrieval. Simply looking at characters is very shallow processing; writing and *constructing* them is relatively deep. This is the Modality Effect.

Explaining how things work and showing others or doing a task is also a much better way to remember things than just reading about them; in the case of remembering Chinese Characters there's less you can *do* other than write them, but practice methods like writing a brief paper can help you learn to use them. This is why essays are a common task in language classes.

Note however that Transfer-Appropriate Processing is also relevant: retrieval is more likely when we attempt to retrieve information in a similar or appropriate context to when encoding occurred. Therefore writing symbols could arguably be a bit less appropriate way to learn to *read* symbols; however it is an extremely relevant way of learning how to write and *construct* those symbols.

I've found some general reference sites eluding to this effect such as this post on Lifehack: Writing and Remembering: Why We Remember What We Write, but could not find experimental results supporting this specific idea. I know my advanced course on Memory covered this specifically but I don't recall exact studies.
> 69 votes

# Answer
I'm going to disagree with Ben here. My colleague Adam Putnam has spent several years researching whether it's best for memory to speak, write, or even think particular responses out loud. His research has continued to turn up no differences between these different modalities, despite what we know about transfer-appropriate processing and elaborative encoding. He has a paper in preparation on the topic, and I'll be sure to link it in should it be accepted.

Other research on the production effect, however, does suggest that "producing" a response should lead to better memory than just reading it. Theories suggest that producing a response increases the distinctiveness of that particular memory. Distinctiveness has less of an effect, though, when the same manipulation is applied to multiple items (e.g., the produced memory is less unique if surrounded by other produced memories). There are several theories out there that explain why this might be.

Our lab's research, though, on the bottom line, shows that it's not the way that you record your answer inasmuch as whether or not you're testing yourself as you do so. For instance, consider the Chinese character you want to learn, imagine it, and then check yourself -- that should be very similar to considering the character, writing it down, and then checking yourself.
> 34 votes

# Answer
The behavioral output itself can only indirectly affect memory, but the mechanism of reinforcement lies in its reception of attention. For instance, athletes who practice a sport seriously know, as also popularly attested by Mack and Cassteven's Mind Gym, that 50% of practice should be mental. They should watch the sport, imagine playing the sport, think about how they want to improve, think about winning, etc. It doesn't matter if the sport is physically practiced or imagined, as long as there is attention.

The route that monotonous rehearsal plays in memory is in forcing attention onto the content, and it most likely is a better strategy than, say, watching TV; however, that doesn't mean that other strategies for enhancing memory aren't far more superior. For instance, as Ben said, the deeper something is encoded - embedded with meaning - the more likely it will be learned.
> 5 votes

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Tags: cognitive-psychology, memory, writing, encoding
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# Question
Title: Controlling for response bias in a forced choice memory task
I want to present participants a pair of items $a$ and $b$, each with an association $x$ or $y$. Later on participants will presented with the items singularly, and asked 'what was the association?'. I'm interested in differences in their memory for the association, between levels of the association.

As I've specified it there is no way to separate differences in memory performance between levels from response bias, because being incorrect on association $x$ means that another response for association $y$ is recorded. Signal detection methods seem to give me an overall measure of discriminability between the two and bias, but can't tell me if the bias is due to genuinely improved memory for $x$, or simply a predisposition to respond $x$.

**What is the best way to deal with this?**

**Initial thoughts:** I'm considering including previously unseen elements into the memory task and getting a measure of response bias that way.

---

Here is some random example data to help with thinking:
```
choice X | X    choice Y | X   choice Y | Y   choice X | Y
   18               18         18              18
   24               12         18              18
   30                6         14              22
   29                7         14              22

```

# Answer
> 4 votes
Let's start with signal detection methods. The big one in memory literature is D-Prime analysis (hits versus false alarms). If the subject chooses X more times than Y, you can compare the number of times choice X is made correctly versus chosen incorrectly (as a false alarm). If that was your paradigm, then choice Y would be the correct rejection (if correct) or a miss (if incorrect).

With this in mind, you can add some degree of confidence to your paradigm. Instead of only two choices, x or y, you can give for options (1 - definitely x, 2 - probably x, 3 - probably y, 4 - definitely y). Never give the option to say, I don't know, because subjects can be unaware that he or she knows the answer, and studies show subjects can be greater than chance through *unconscious recognition*. Then, if you're afraid of a side bias, extracting only "definitely" answers should be a way of excluding that possibility, because if they were just guessing they would choose the "probably" answers.

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Tags: memory, methodology, experimental-psychology, statistics
---


# Question
Title: Is it possible to measure the working memory of a non-human animal?
Is it possible to measure the working memory of a non-human animal? And if so, have there been any studies that have quantified the working memory of animals, and that have compared that to the working memory of humans? Or are the two not comparable?

# Answer
Sure. For example, working memory can be assessed using the **delayed match to sample** task. Here are examples from monkeys, rats, pigeons, and bees.

The problem with **comparing them** is that the actual stimuli used for each species are different (e.g. odors for bees, shapes for monkeys) and this is known to affect the results.

In humans, if you run similar tasks, just with small verses large sets of possible stimuli, for example digits verses general words, you can get very different results. Even if you did try to use the same stimuli set, the result will probably not be "subjectively" equal to that of a different species. Think of yourself trying to do the odor task of the bees; it's not a fair game.

Other seemingly small changes in the paradigm can also affect the results, for example a delay between the trials, etc. So the only way to seriously compare them would be to conduct the same experiment, by the same lab, of different species. I personally don't know of any research that was directly aimed at comparing them. Maybe someone using (lesioned) animals as a model for dementia would know more.
> 12 votes

# Answer
Sure, visual working memory capacity has been assessed in humans, chimps and mac using a change-detection tasks and trail-making tasks.

For example, the chimp Ayumu at Kyoto University easily outperforms all humans on a simple number sequencing task. In the task, the numbers 1-n appear briefly on the screen in random positions and then the numbers must be touched by the participant in numerical order. Ayumu can sequence more than nine digits in less than 200 ms, according to the 2007 paper. In contrast, human performance was at chance levels at that exposure duration.

In another visual working memory task, the change-detection task, colored shapes appear on the sample screen, disappear for some brief amount of time (typically about a second) and then reappear. 50% of the time all the squares are the same, 50% of the time one square has changed. The subject indicates if a the test screen matches the sample screen. This a delayed-match-to-sample task. To measure memory capacity, the sample and test array sizes are increased, 2,4,8, etc. Humans and rhesus perform equivalently on this task, in that both species are able to perform at or above 80% correct for array sizes of about 3~4 items. earl miller study

io9 published a pop-sci discussion of the chimp study, *"This chimp will kick your ass at memory games — but how the hell does he do it?"*, and links to a flash game by Lumosity Games that replicates the original study.
> 8 votes

# Answer
When classes come visit the Duke Canine Cognition Center, we ask them how they would test the memory of their pet. The kids come up with a solution pretty similar to how its done. One kid put down 5 different cups, showed the dog a treat, and placed it under one of the cups. Then the dog was either distracted, or simply restricted from approaching the cups, for a fixed amount of time. The dogs are very eager to retrieve the treat, and will often just stare at the cup until the time has elapsed, so in another version we shield the cups with a giant occluding board so the dog must keep an *internal representation*. This task is no problem for many dogs. We do 20 second, 40 second, and then 60 second trials with only 3 cups, and there is a lot of variability in success.
> 1 votes

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Tags: animal-cognition, memory
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# Question
Title: What is the mechanism explaining the effect of a positive attitude on immune system functioning?
It seems likely that a positive attitude can speed up the healing process. but I can't decide by what mechanism it would operate by.

### Questions

* Does having a positive attitude improve immune system functioning?
* If so, what is the mechanism by which this occurs?

**Initial thoughts:** Is it the inhibition of some sort of stress cortisol? The answer seems like it would have to do with how the placebo effect or hypnosis suggestion functions.

# Answer
> 6 votes
As far as I know, it has not been shown that a positive attitude has any effect on the immune system (ignoring the less significant placebo effect). What has been shown is that long-term stress has a negative effect on the immune system. Short-term stress actually has a positive effect on the immune system, but long-term stress has been correlated with several affecting mechanisms: lower white blood cell count, too much cytokine production.

The following study found lots of mixed results. A typical sign that there's really no clear answer to the question. When there are so many confounding results, it's easy for people to only take the half they agree with, so we should be wary of our propensity to do so when we want to hear a particular answer.

> The failure of optimism to consistently predict better physical health indicators and outcomes is consistent with this pessimistic view of optimism: “The best doesn't always occur. When things go wrong in a big way, the optimist may be particularly vulnerable.”

...

> I have suggested an alternative hypothesis to explain negative effects of optimism on the immune system (see Fig. 1; Segerstrom, 2001; Segerstrom et al., 2003; Solberg Nes et al., in press). This hypothesis specifies that under difficult circumstances, more optimistic people remain engaged with those circumstances whereas more pessimistic people disengage, avoid, or give up. Giving up can be a physiologically protective response because stressor exposure is minimized in the short term by giving up rather than remaining engaged...

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1948078/

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Tags: physiology, health-psychology, positive-thinking
---


# Question
Title: Computational differences between spiking neural networks and previous ANNs
This is an AI question regarding "3rd generation neural networks" - spiking neural networks (SNN).

I hve been studying this concept online from various papers, mainly Maass (1997). I and am not entirely sure I understand why SNN's are considered pulse-code in contrast to earlier ANN's which are rate-code.

I have background in neuroscience so I understand the terms and ratio, I am asking regarding the actual implementation.

Is the practical difference in the fact that when each neuron updates its current state in an SNN it deals with the entire history of every pre-synaptic neuron and not only the last step? Is that what gives it temporal characteristics which previous generation ANN's lack? What is the key computational difference between SNN and earlier approaches?

### Notes

This question was migrated from SO, and a duplicate was asked on cstheory that was migrated to CS.SE.

# Answer
> 2 votes
Rate-based-network is a specific implementation of the more general spiking-networks. One may see a rate-based-network as a spiking-network in which the inputs from each neuron are accumulated over a short time-period (think of "one second") and are used to update the state of their target neuron only once in each time-period.

For example, if an input neuron has an output of '40' in a rate-based-network, you should think about it as if it fire 40 times in the time-period, and only once in each time-period it's target neuron 'read' this input.

On the other hand, with spiking-neurons the output is limited to binary and hence the time-period used must be shorter than the maximal rate. In each time-period the target neuron updates its state based on it's (binary) input.

So to summarize:
* Spiking networks describe a more general phenomena.
* Spiking networks can react to inputs with fine temporal structure and act in time-periods which are order of magnitude smaller than rate-based-models.

Also one may add that spiking networks are likely to be more accurate biological description of the brain (but still a very rough account).

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Tags: computational-modeling, neural-network, artificial-intelligence
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# Question
Title: Under what circumstances does the brain devote resources to only the "when" of sensory events?
In a recent review article (Arnal & Giraud, 2012), the authors delve into changes in cortical oscillations which assist in predicting the causes of a sensory stimulus (the "what", via predictive coding) and its timing (the "when", via predictive timing).

This allows the cortex to dampen its response to a repeated and/or predictable stimuli so that more "processing resources" can be reserved for other less predictable (and potentially more important) stimuli.

Predictive coding can be modeled using a Bayesian framework, with predictions being made about the "what" aspect conditioned on the reactions to prior stimuli.

In certain circumstances --- intense military march to a drum beat or, for the young, dancing to a bass-heavy song in a nightclub --- it seems to be possible to dampen the "what" aspect *completely* since the Bayesian priors on "what" are near-certainty. **To what degree can the brain move resources from the "*what*" to the "*when*" to achieve a precise level of timing for conversion between sensory and motor output?**

> Arnal, L.H., Giraud, A-L. (2012) Cortical oscillations and sensory prediction. *Trends in Cognitive Sciences 16*(7), 390-398.

# Answer
**To what degree can the brain move resources from the "what" to the "when" to achieve a precise level of timing for conversion between sensory and motor output?**

I think that you may be making a false assumption here. I don't think that the 'what' and the 'when' are in competition for resources. According to Arnal and Giraud (and many others), having a valid prediction of when an event is going to occur *and* having a valid prediction on which event is going to occur, *both* lead to reduced primary sensory activity (and to a shortened reaction time). As such, you could say that the resources that go into making both types of predictions (the 'when' and the 'what'), reduce total resources used. In the opposite situation, where there is an invalid prediction, there is not only more total neural activity in primary sensory areas, but stimulus representations are also less sharp (Kok et al., 2012).

Furthermore, the differences seen in frequency space that are related to 'what' and 'when' predictions, as well as the fact that 'when' predictions seem to have a necessary stimulus-driven component while 'what' predictions do not, also point to a possible dissociation in resources used. In other words, it might not be the same neurons firing anyway. As an example, Wacongne et al (2012) suggested a model on how the feedforward and the feedback portion of predictive coding (of 'what' predictions) might work using different neurons within a single cortical column.

Finally, less resources does not necessarily translate to better sensory-motor conversion: selectively attending to a stimulus increases the amount of sensory brain activity, but decreases reaction times. It seems that it might boil down to how sharp the stimulus representation is (which is connected to valid/invalid 'what' predictions), followed by how strongly these neurons are firing (which is connected to selective attention). Squandering resources would mean having the wrong neurons firing, rather than firing more vs. less in a given sensory area. Once again, this would mean that forming any type of prediction leads to better use of total resources.

I'm still not sure if this answers your question, as the examples you give (e.g. drum beat) contain certainty on both the 'what' (sound of drum) and the 'when' (time of sound onset). If you want to dissociate the two, you could have a situation where you know what is going to come (sound of drum) but with a jittered stimulus onset asynchrony. Or, you could have a precise timing with novel sounds (a sound of a different pitch is displayed every half a second). In those cases your predictions would be mainly on the 'what' vs 'when', but in both cases hearing any of these sounds would carry an element of surprise, and would therefore lead to more primary sensory activity and a longer RT, i.e. more resources would be used.

**References:**

> Wacongne C, Changeux JP, Dehaene S (2012) A Neuronal Model of Predictive Coding Accounting for the Mismatch Negativity. *The Journal of Neuroscience* 32:3665-3678.
>
> Kok P, Jehee JFM, de Lange FP (2012) Less is more: Expectation sharpens representations in the primary visual cortex. *Neuron* 75:265-270.
> 4 votes

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Tags: sensation, bayesian, synchronization
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# Question
Title: Utility or software to visualize Neural Network?
I am using Octave to generate a Neural Network with a single hidden layer, and saving it as two CSV files.

Is there a utility or software that will load the files and create an image, PDF or HTML page that displays the weights over edges connecting neurons?

# Answer
> 3 votes
If you have CSV files a quick way to generate images would be to open it in Excel (or a similar spreadsheet software) and use some sort of colour scale conditional formatting (under home\>styles in Microsoft Excel) - set the width and heights of the cells to small in order to view all the data at once.

You could also use a surface chart in order to visualise the data in Excel.

Otherwise if you are familiar with a tool like Matlab or R, you might wish to use some sort of graphic tool to represent it, e.g. meshgrid in Matlab might work.

Matlab and/or R can be programmed to load several CSV files and create graphics from them. The first two techniques I mentioned (although accessible to a more novice computer user) have to be carried out manually.

# Answer
> 1 votes
For what it's worth, I did a lot of research and did not find a solution.

So I created my own using HTML, jQuery and a canvas. It's not pretty, but it does not require a lot of work because the functionality is simple: When you click on a node, display its edges and the associated weights.

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Tags: methodology, neural-network, software, connectionism
---


# Question
Title: Does teaching a bird an artificial task like eating from a feeder hurt its performance in the wild?
Can training a wild animal through operant conditioning somehow cause the animal to forget or be unable to perform tasks which it had perviously learned?

Is it likely that training wild animals through operant conditioning would somehow cause them to be unable to learn or retain other skills? Or is that not how learning actually works?

Does teaching a bird an artificial task like eating from a feeder hurt its performance in the wild?

# Answer
> 10 votes
I wouldn't worry about "running out" of room in our brain. We often forget things just because *we don't need to know them*, similar to . There are plenty of human savants that display apparently "unlimited" capacities of certain forms of memory, such as Hyperthymesia where one has a seemingly perfect amount of recall of autobiographical details (not to be confused with the largely debunked notion of "photographic memory").

It appears we forget things not because we're low on space, but because we don't need that information (not that there's intent, it's just practical). Information often accessed is strengthened, information never used is weakened and lost. Similarly we physically prune neurons and connections we no longer use in Synaptic Pruning.

Back to the issue of survivability; it's possible that operant conditioning a wild animal could cause them to incorrectly react to natural stimuli. The biggest risk here would be Generalization of stimuli, like Little Albert becoming (temporarily) afraid of all things white and fluffy instead of just the rat he was conditioned with. If you trained a dog that brown furry things means I should attack and he generalizes this to a bear, it won't end well for the dog of course.

This would generally be less of an issue than you might fear however; an animal will quickly forget the conditioned response due to Extinction provided the Conditioned Stimulus is no longer paired with the Unconditioned Stimulus. Repeated exposure of the CS with no US will eventually extinct the reaction; reinforcement learning goes both ways.

It's even more unlikely that completely artificial conditioning will result in prolonged harm to survivability. This is because if the Conditioned Stimulus is never presented, the conditioned response will simply not be activated. The CS won't even need to be extincted, the animal would likely just forget eventually.

Now the one thing I would worry about is Extinction of *natural* defense/predatory responses. If an animal has learned through experience to do or avoid doing something and, through domestication/etc they no longer feel the urge to run from predators it will of course impact their survival.

It's impossible to say one way or another really, but I hope that helps you understand what's potentially at work here.

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Tags: learning, conditioning, animal-cognition
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# Question
Title: Which type of stimulus results in an optimal learning curve for rats and mice?
When using operant conditioning to train mice or rats, what type of stimulus is most effective? For example, does a negative reinforcement of a loud noise have a more profound effect than a negative reinforcement of pain? What about for positive reinforcement? Is pleasure more powerful than food? Which type of stimulus is considered optimal for learning?

# Answer
> 7 votes
First, the concept of optimality of a learning curve is not well defined. You can measure at least 3 different aspects of learning:

1. Speed of learning
2. Time before extinction
3. Performance at peak

Of course, there may be other measures as well, and any combination of such measure may also be a legitimate measure for certain uses.

**Conditioned Taste Aversion (CTA)** is a form of learning in which animals (and humans) learn to avoid a type of food after consuming it and suffering symptoms resembling food poisoning shortly after. **In certain cases, the learning can take a single trial, cause the animal to completely avoid the food, and last for a lifetime \[1\]**, making this an optimal learning in all of the above 3 measures.

However, CTA is a very special and specific type of learning, and won't help you in teaching your rat to walk in a maze... **I haven't found a methodological comparison of different types of reinforcements, and I suspect such a comparison might be very difficult or even impossible**, because the efficacy of a (positive) reinforcement is greatly affected by the animal's "appetite" for it: for example, to use food as a reinforcement, rats are usually starved (the technical term is "maintained on a food deprivation schedule") for a few days. To use water as a reinforcement, rats are kept on a water deprivation schedule. How would you equate the subjective level of starvation and thirst?

Other aspects of the learning schedule have been studied more thoroughly. For example, to produce a long lasting learning (increase measure #2) at the expanse of speed of learning (measure #1) and peak performance (#3), you can provide partial reinforcement: reinforce the animal only on some of the trials \[2\].

---

\[1\] Conditioned taste aversion: Memory of a special kind. Bures, Jan; Bermúdez-Rattoni, Federico; Yamamoto, Takashi; Oxford University Press, 1998 doi: 10.1093/acprof:oso/9780198523475.001.0001

\[2\] Partial reinforcement: a review and critique. Jenkins, William O.; Stanley Jr., Julian C; Psychological Bulletin, Vol 47(3), May 1950 doi: 10.1037/h0060772

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Tags: learning, animal-cognition, conditioning, behaviorism
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# Question
Title: How is the size of a video related to its perceived quality?
Video is often presented at different sizes. On the Internet, many websites provide quite a few size settings. In the store, you can buy TVs of many different sizes. In both cases, it's the same resolution video being stretched to a various sizes. To the technically savvy, making the same pixel occupy a larger physical space does not increase the quality of the video. But to the average consumer, he may think bigger is better.

What does the graph of perceived quality VS physical size look like? Is it linear, that is bigger is always better. Or is it parabolic? That is, there is a perfect ratio of pixel to size and any deviation from this ratio will result in a worse perceived quality. Or is it some other shape?

# Answer
> 16 votes
At least for images (I don't know of such a result tested on videos) for a given resolution, there is an optimal display size (assuming constant viewing distance. otherwise, display size should be measured in angles from the viewers point of view). In a paper from 1989, Peter Barten provided a formula to compute this effect <sup>\[1\]</sup>. The gist can be seen in the following figure from that paper:

For the low resolution images (e.g 100px wide) there is a slight advantage in quality ranking for the smaller screen over larger ones. However, as the number of pixels increases, the perceived quality on the small screen saturates, and larger screen are preferred.

---

\[1\] The Effects of Picture Size and Definition on Perceived Image Quality. Barten, P. G. J; IEEE Trans.on Electron Devices, 36 (9), p. 1865-9, Sept.1989 doi: 10.1109/16.34260

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Tags: perception, vision
---


# Question
Title: What psychophysical research published its data?
**Can you point to published research in psychophysics that made its original\* data available?**

\*by 'original' I mean the trial-by-trial responses for each subject, and not some kind of aggregate that is usually reported (such as overall percent correct for each condition, or even each stimulus pair).

I am specifically interested in *discrimination* studies, using *2-alternative-forced-choice design*, but any other psychophysical work is also welcome.

I'm aware of this great question and went over its answers when looking for data. It seems the published data in those datasets is mostly social science, "soft" psychological data and imaging data, and I found only few psychophysical studies, none of them involving discrimination tasks.

# Answer
It's not exactly what you're after, but the Newcastle Cognition Lab has a data repository. It includes a number of learning curve datasets and other studies that measured response time to various simple cognitive tasks.
> 3 votes

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Tags: reproducible-research, data, psychophysics
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# Question
Title: Do the Jungian Cognitive Functions/ Processes really exist?
**Background**

Many of us must have come across personality theories like MBTI which use part of Carl Jung's concepts to make a theoretical system used to divide people into *types*. For example, MBTI says that *if* the person is not neurotic or something like that, *then* he/she must fall into one among the 16 personality types that have been defined. Over simplification of the MBTI over the Internet has made the base of this theory unknown to many people, but talking about that in this question helps nobody.

MBTI as taken by psychologists, seems to be centered more around the concept of Functions more than the four letter model. Typing a person is done generally after recognizing their *Dominant* function. Some psychologists seem to have made their own different models about these Cognitive Functions (like John Beebe and Lenore Thomson for example). Some claiming 8 exist in the human Psyche, and some claiming 4 exist, some saying they gradually develop, some opposing the views and so on...

Recently, I have come across a Youtube video in which a researcher claims to have made this theory scientifically observable and researchable - and seeing that this video has been made at Google Talks makes it believable.

I think Jung's concepts - which are based on observation, introspection, Energy flow etc. seem to be somewhat like Pseudoscience to any scientific mind. However, after watching this video I started to wonder whether what he says is really true or not?

**Additional Material**

* An extract from Carl Jung's Psychological Types where Jung speaks about these types.
* An online forum where each personality type profile exists as a sticky thread in its own subforum. These profiles use what seems like a modified version of the Cognitive Functions concept.
* EDIT: What Dario Nardi speaks about in the video is essentially an outline of what he published in his book. I have found a forum post where a summary of material he published in his book has been written. Please take a look at it if you don't have time to watch the whole video. Here's the link to the presentation he shows in the video (a pdf file).

**Questions**

* Short version: Is the evidence quoted in the above source (the forum link) a valid evidence to support a concept like Cognitive Functions as described by Jung?
* Long version: There are two main things in the above source (the forum link) that I want someone to confirm as a proper evidence.

Firstly, as quoted by the source above, Nardi speaks about various regions in Neo Cortex region where he placed these EEG sensors. From what I have read, it seems that he mapped the regions to some activities.

>

Here's what he says about these regions is like:

> Fp1 "Chief Judge" (is used when/to)
>
> * Provide a reason
> * Decide between options
> * Detect an error

Writing all of them here would make this question look like a book, but I want to know whether all this is as rigid as it looks or not. I want to know where Nardi is making a mistake in this research. (There could be some activities which might have been mapped wrongly, or those which have deeper mechanisms in brain rather than just in Neocortex region.)

Secondly, I will not be long here, but there is a similar part where he speaks about various patterns (in regions of brain "lighting up") he observed during this observation. Although asking for an evidence to this would be basically an extension to the first question, but my question here would be whether such patterns (not necessarily the same ones) have ever been classified/suggested in literature already?

Lastly, (this might be rhetoric question) if the answer to the above question is affirmative, Does this imply that theories like MBTI are really valid, and that there are really types among people's brains? (Nardi tried to map those patterns into types of people, as I said their dominant function)

# Answer
> 3 votes
The research done by Dardio Nardi (the researcher you're referring to) clearly shows that something is there. Although, he would have no way of knowing as to whether his samples were of the particular type, or if what's being demonstrated really demonstrates use of that particular cognitive function. E.g doing something logical doesn't necessarily mean you're 'using' Ti.

I do believe we have innate, instinctive preferences and can classify them into types as such, but I truly doubt that Jung's work would be 100% accurate. Even Jung was hesitant to be exacting in his understanding of the psyche - which lead him to leave a lot of holes in his model.

Myers and Briggs filled those holes with many assumptions - which is why the functions are a far better application to finding somebody's 'type'.

So yes, I would say that they do exist. But probably not exactly in the way they were described by Jung. Hopefully people begin to think critically about this, then maybe we can actually see some results.

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Tags: personality, measurement, jung
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# Question
Title: What makes the difficulty of an arithmetic item? The operation or its length?
When presenting someone with an arithmetic item, let's say 2+2, what makes it difficult? Is the item 2+2+2 only longer, or also more difficult?

Does the mental operation of addition make the difficulty, or also the amount of mental operations? Or should the amount only be seen something influencing the length it takes to solve the item, but not it's difficulty?

Are there any publications that address the idea of difficulty for psychometric items which address this question?

# Answer
> 6 votes
Difficulty of an item could be operationalised in a variety of ways: probability of getting the item correct, amount of time required to complete, amount of resources required to complete, etc.

### Item response theory perspective

That said, in the item response theory literature item difficulty is typically synonymous with a parameter related to probability of getting an item correct. For example, in a basic three parameter logistic model, you might have a an equation like follows:

$$ p\_i(\theta) = c\_i + \frac{1 - c\_i}{1 + \exp(-a\_i(\theta - b\_i))} $$

where $\theta$ indexes individual ability, $c\_i$ is a guessing parameter for item $i$, particularly relevant for multiple choice items, $a\_i$ is the degree to which the item discriminates between individuals, and $b\_i$ indexes item difficulty.

Of relevance to your question, this model asserts that the probability of getting an item correct is related to a number of factors including the ability of the individual and the difficulty of the item.

More complex models would permit individual by item interactions, where for example some individuals are better at math problems where as other are better at language problems.

### Cognitive psychology perspective

Another perspective on item difficulty comes from cognitive psychology. We might alternatively call this feature of an item, its *complexity*. From such a perspective we could analyse the component processes of the task to develop a model of its complexity. From this perspective, `2 + 2 + 2` is more complex than `2 + 2` because it generally requires more operations to solve. E.g., an individual needs to first solve `2 + 2` as a subtask, store that value in working memory, and then `add 2` to the stored value.

However, I think a cognitive strategy learning perspective provides further insight. Ultimately, it may be the strategy that has a particular complexity rather than the item per se. And strategies are acquired with practice and training. For example, when a young child solves the problem `2 + 2`, they may have to apply the somewhat complex strategy of recognising this as an addition problem, counting fingers `1 and 2`, then counting two more fingers `1 and 2` and then counting all the finger `1,2,3,4`. Alternatively, when most adults see `2 + 2`, they are able to immediately and reliably retrieve the correct answer from memory. Or for example, if you are able to use a calculator, the difficulty of multiplication of large numbers is dramatically reduced.

There is a large literature on what is sometimes called algorithm-retrieval shift. I summarise some of this literature in my thesis (Anglim, 2011). To read more, you could check out Delaney et al (1988) or perhaps some of Robert Siegler's work (e.g., Lemaire and Siegler, 1995; he has a huge amount of research on strategies used in mathematical problems). I'd also encourage you to check out some of the many articles using the ACT-R framework (see below). The main point is that over time, complex tasks become simplified as individuals optimise knowledge, strategies, and task representations to the task domain.

From such a perspective, 2 + 2 is easier from 2 + 2 + 2 for a number of reasons. It is simpler in terms of the typical strategies that are used, but also the structure of typical task environments means that `2 + 2 + 2` will be less frequently encountered than 2 + 2. Thus, individuals are more likely to switch to a retrieval process on 2 + 2.

### Summary

* complexity and difficulty are strategy specific
* the environment influences task and strategy learning
* and thus, the environment can influence experienced complexity and difficulty

### References

* Anglim, J. (2011). Strategies in skill acquisition: reconciling continuous models of the learning curve with abrupt strategy shifts. PDF
* Delaney, P. F., Reder, L. M., Staszewski, J. J., & Ritter, F. E. (1998). The strategy-specic nature of improvement: The power law ap- plies by strategy within task. Psychological Science, 9(1) 1-7.
* Lemaire, P., & Siegler, R. S. (1995). Four aspects of strategic change: Contributions to children's learning of multiplication. Journal of Experimental Psychology: General, 124 , 83-{97.
* Robert Sigler: See website for many publications with free PDFs http://www.psy.cmu.edu/~siegler/
* ACT-R Literature on Mathematical Problem Solving: http://act-r.psy.cmu.edu/publications/index.php?subtopic=22

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Tags: mathematical-ability
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# Question
Title: To what extent are correlations of father's age with birth defects and autism causal?
I read the following in the paper today:

> Dr Karin Hammarberg ... said that while most children are born healthy, **large studies of parental age were starting to show higher rates of birth defects and autism in children born to men over 40**.
>
> A recent review of paternal age published in the Asian Journal of Andrology said an American study of 132,000 men found children of those over 45 were nearly six times more likely to have an autism spectrum disorder compared to children born to men under 30.
>
> The review also pointed to a Dutch study of 60,000 births which found children born to men over 40 were three times more likely to have autism and a US study of 5 million births which showed men over 50 had a 15 per cent higher chance of having a baby with birth defects including congenital heart disease and cleft palates.

However, my first thought was that the age of the father must be highly correlated with the age of the mother. Thus, an alternative explanation is that the higher prevalence of birth defects for older fathers is due to the fact that older fathers typically have babies with older mothers. Of course, the same argument could be made for the reported higher prevalence of birth defects in older mothers (i.e., they're having babies with older fathers).

### Questions:

* To what extent is paternal age associated with prevalence of birth defects after controlling for maternal age?
* To what extent is any association between paternal age and prevalence of birth defects causal? (maternal age is the main covariate that I could think of, but there might be other important confounding variables)

# Answer
This is a partial answer suggesting a possible causal mechanism.

One of the factors leading to birth defects and autism is mutations in the parent's genetic material. In a recently published article, Sun et al. (2012) observed that:

> The paternal-to-maternal mutation rate ratio is 3.3, and the rate in fathers doubles from age 20 to 58, whereas there is no association with age in mothers.

In other words, while the mother's age will not have an effect on the number of mutations passed to the offspring, the older the father the more mutations. That means a possible causal mechanism for correlations of father's old age is an increase in the number of mutations (most of which are neutral or detrimental) passed to the offspring.

Kong et al. (2012) explain the connection of *de novo* mutations (of the sort observed by Sun et al. (2012)) to autism and other disorders more clearly. This blog post suggests why fathers might produce more mutations:

> The difference probably comes from the distinct biology of male and female reproduction. Cells that give rise to sperm cells continuously divide throughout a man’s life while cells that develop into ovules stop replicating when the woman is still a fetus. Consequently, an ovule at any time of a woman’s life will have gone through 24 cell divisions while sperm will be at about 200 divisions in a 20 year old man and up to 600 in a man of 40 years. When cells divide, they replicate their DNA to transmit a copy of the genome to each daughter cell but this replication is not 100% accurate. With each division mutations creep in the DNA so the more divisions a cell goes through, the more mutations it accumulates.

### References

Kong, A., Frigge, M.L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S.A., Sigurdsson, A., Jonasdottir, As., Jonasdottir, Ad., Wong, W.S.W., Sigurdsson, G., Walters, G.B., Steinberg, S., Helgason, H., Thorleifsson, G., Gudbjartsson, D.F., Helgason, A., Magnusson, O.Th., Thorsteinsdottir. U., & Stefansson, K., (2012) Rate of *de novo* mutations and the importance of father’s age to disease risk. *Nature* 488: 471-475.

Sun, J.X., Helgason, A., Masson, S., Ebenesersdóttir, S.S., Li, H., Mallick, S., Gnerre, S., Patterson, N., Kong, A., Reich, R., & Stefansson, K. (2012) A direct characterization of human mutation based on microsatellites. *Nature Genetics* \[press\]
> 10 votes

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Tags: developmental-psychology, aging, autism
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title: Measuring meta-intelligence

text:
# Question
Title: Measuring meta-intelligence
Does anyone know of any research in measuring metacognitive abilities (i.e. metacomprehension, metamemory, meta-emotions(?), etc) in people? In other words, I'm wondering if the same way we have IQ tests (which I know is a whole other topic of debate), if there would be a way to measure "meta-IQ"?

# Answer
> 5 votes
A good overview on the topic is Metacognition: A Literature Review (E. R. Lai), page 27 has a section assessing the measures of Metacognition.

> Flavell (1979) describes assessment tasks that asked children to study a set of items until they were sure they could remember them completely. Children were then tested on their ability to recall all the items.
>
> Another common task was to read a set of written instructions and indicate any omissions, mistakes, or areas of ambiguity. Schneider (2008) observes that the most studied type of procedural metamemory is self-monitoring. Assessments designed to capture this ability include ease of learning judgments, judgments of learning, and feelings of knowing. For example, ease of learning judgments typically ask students to study a set of test materials for a short amount of time and then assess their abilities to remember the material. After the students are tested on the material, their performances are compared to their initial predictions.

Generally assessments focus on one specific area of Metacognition like Metamemory.

See also Development and Validation of an Objective Measure of Metacognition that assess four studies evaluating metacognitive abilities.

Searching around on Google Scholar finds a great deal of studies using and proposing various measures for Metacognition. There's certainly no "standard" like an IQ test, as Metacoginiton: A Literature Review notes, part of the challenge in studying and teaching Metacognitive abilities is due to the lack of focus on them in traditional school curriculum.

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Tags: measurement, metacognition
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# Question
Title: Can processing effort for sub-tasks in neural networks be measured?
I often heard statements like:

> 80% of your brain processing is computing the effect of gravity

or, similarily:

> You only use 20% of your brain power

My question isn't about the truth of these statements but if they are well-formed: can we measure 'processing' in the brain (or a sufficiently complicated artificial neural net) to quantify how much of the processing resources are allocated towards specific sub-routines?

As an example of when this is doable in another domain: consider a computer with a standard von Neumann architecture. In this case we can tell how much processing goes into sub-routine by simple counting the number of steps each subroutine holds the processor. However, this simple counting is only possible because of two features:

1. There is a clear central processor, and data is not transformed by anything except it.
2. There is a clear duality between software and hardware allowing us to identify when a specific sub-routine (software) is being allowed access to the processor (hardware).

Both features are missing in a computer with a neural architecture. **How can we measure the resources that a computer with neural architecture (example: the brain) devotes to subtasks?**

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### Notes

I am interested in settings where there isn't an obvious localization of sub-tasks. So an answer like:

> we can measure the amount of resources that go towards recognizing faces by looking at the metabolic uptake of the fusiform face area.

Is not that interesting to me, since it is only valid for sub-tasks that happen to have specially-devoted areas. Of course, if there is an argument that any reasonable (or more restricted: human-like) neural-architecture *has* to compartmentalize its computations then I would like to hear that. However, the answerer would be left with the task of explaining how to identify the group of neurons that should be associated with a specific sub-task.

# Answer
> 3 votes
Well firstly, what are those statements really saying? How do you measure "processing" or "power" as it relates to the brain? For an electrical engineer working in communicatons, it's easy: you just take the square of the amplitude of the signal (signal power) or count the number of instructions per second (processing power). But that's the discipline where processing power is defined; making an analogy to a brain brings a lot of caveats. What's an instruction? How many little instructions can you break one instruction down into? Where do you want to draw the line in a color spectrum that divided orange from yellow? Or do you want to draw more lines and have dark and light yellow? Or yet more lines...?

Hans Moravec, a machine intelligence researcher, is famous for his comparisons of technology to organismal processing power. Here he explains a little bit about how he comes up with his numbers, but they're really not satisfactory to me. He seems to take one example (the retina) and judge it by what it can do empirically with an image, then extrapolate from there to the rest of the brain. So this only considers a single network topology in a system that has millions more variations in topology.

The major problem that is a typical complaint by biologists when people use the computer science analogy for brains is that metabolism and functions are too closely coupled to easily separate. Functional mechanisms can occur as negotiations between molecular networks (including genetic transcription) in addition to the electrical signals that electrical engineers and computer scientists generally think of as "processing".

This is especially outlined in the glutamine, gaba, and adenosine molecular networks (i.e. the transmitters are closely coupled to metabolism through ATP and the Krebb cycle). A lot of recent evidence has also put a larger emphasis on astrocytes. This paper is about epilepsy, but takes some time in the introduction to develop ideas about astrocytes and brain metabolism complete with references. The brain-metabolism material is typical in any neurobiology text book; astrocyte participation is a more recent line of research. There's also still a lot of research coming up in molecular mechanisms for memory.

There have been all kinds of measurements on processing power, including at the genetic level, but all these measurements make an assumption about what a bit is by breaking biological subsystems into two states (this, 1 and 0). But then later down the line, somebody will find that there was actually a third significant functional state. So it's all about where people want to draw lines.

Another problem (more at the macro level now) is that the same task will have different processing requirements depending on how robustly the organisms internal model is approximating and predicting the external world. So a task that you know what to expect for will take considerably less "processing power" than one where your expectations are not met. Karl Friston wrote an interesting review suggesting a modeling framework that might help to explain this.

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Tags: neuroscience, measurement, computational-modeling, neural-network, theoretical-neuroscience
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# Question
Title: How does body temperature and oxygenation affect thinking ability?
I'm interested if the brain works better when the temperature is higher than usual and the amount of oxygen in the air is a bit lower than in fresh mountain air. This has been my personal experience.

# Answer
> 7 votes
**Warmer temperature** are shown to raise aggression level (Anderson, et al., 1995). Citing this study, DeWall & Bushman, 2009 found a similar correlation between words associated with high temperatures and hostile behavior. This could be perceived as a threat to clear thinking.

Moss & Scholey, 1996 shows **oxygen administration** increases memory. *However*, **intermittent hypoxia** on developing children led to *adverse* effects (both mental and physical), according to Bass, et al., 2004. Though, I must say, you can't really determine the oxygen content indoor vs. outdoors without sensors, even if you raise in elevation and who's to say what competing particulates there are between the two environments?

It's known that kinetic motion itself increases neurogenesis, mostly in studies with exercise, like this one. There's been a lot of papers and laymen articles on the subject of exercise and neurogenesis lately. The act of walking or climbing the mountain might contribute a lot to the subjective experience of thinking.

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Tags: neuroscience, physiology
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