Latest revision as of 09:27, 1 April 2024

The account of this former contributor was not re-activated after the server upgrade of March 2022.

Notes to self

Bookmarks

more here

Within CZ

Bot support

Implemented

See also the list of scripts I ran.

create related articles for clusters that lack them: Category:Bot-created Related Articles subpages
fix double redirects

Just a thought

May be useful to

create definitions for clusters that lack them
check whether the length of definitions fits a given size
help with Eduzendium
create pages for existing categories whose page has not been created yet.
move Template:XYZ-Article:Metadata to Metadata:XYZ-Article
check for the correct setup of user pages
create missing talk pages, as per User:Daniel Mietchen/pwb/notalk.py
organize geographic articles, e.g. on U.S. states
lemma bot
a job subpage to revolutionize job searching?? Would of course require that at least all of the most popular job search terms have at least a cluster

Charter

Within WP

Wikipedia:We aren't Citizendium
Wikipedia article traffic statistics
A template helping to identify redirect pages
WikiMindMap — may help with Related Articles
bookshelf - comparison of WP and EB
Wikirage
Diberri:Bot-assisted medical template filling
icon template
DOI bot

sample edit

Citation bot

Template:Emergency-bot-shutoff
Reference wikification
Size of English Wikipedia broken down
Wikipedia Autoreviewer (Beta Version), now here
Find link — finds related articles
Calls for experts
Most vandalized pages and a list of vandalistic edits used to train an artificial neural network behind Cluebot; another example is here
examples for vandalism extending to non-controversial topics, e.g. Kugelflächenfunktionen (spherical harmonics), Krl Guttenberg and Outline of physical sciences
Source and temporal provenance (using color schemes). See also this post on color-coding reliability as a function of number of survived edits and this tool which actually implements it for any Wikimedia-powered wiki. Maybe something for CZ, too?
Links to CZ from WP (en)
Graphics Lab - for anything concerning images
nutshell template
Math formatting
animated image of an echidna
discussion of Special:LinksFromHere

Featured articles
Good articles
Possibly unfree images
Retired Wikipedians
Protein Box Bot - source code
http://en.wikipedia.org/wiki/Sneeze#Traditional_responses_to_a_sneeze
Study of vandalism survival times
List of external links from WP to CZ
Strategic Planning program
A search box to search archives specifically
Some suggestions on how to improve the (German) Wikipedia
some useful forms and template scripting
School and university projects that use WP for coursework
WikiMiniAtlas - allows for interactive display of a map, as here; also check this for line break problems after <span>
purge page cache for UTC display
The value of Wikipedia — see also this discussion

MediaWiki extensions

Full list. See also the MediaWiki feature list.

ABSTRACT: BACKGROUND: Wiki technology has become a ubiquitous mechanism for dissemination of information, and places strong emphasis on collaboration. We aimed to leverage wiki technology to allow small groups of researchers to collaborate around a specific domain, for example a biological pathway. Automatically gathered seed data could be modified by the group and enriched with domain specific information. RESULTS: We describe a software system, BioKb, implemented as a plugin for the TWiki engine, and designed to facilitate construction of a field-specific wiki containing collaborative and automatically generated content. Features of this system include: query of publicly available resources such as KEGG, iHOP and MeSH, to generate 'seed' content for topics; simple definition of structure for topics of different types via an administration page; and interactive incorporation of relevant PubMed references. An exemplar is shown for the use of this system, in the the creation of the RAASWiki knowledgebase on the renin-angiotensin-aldosterone system (RAAS). RAASWiki has been seeded with data by use of BioKb, and will be the subject of ongoing development into an extensive knowledgebase on the RAAS. CONCLUSIONS: The BioKb system is available from http://www.bioinf.mvm.ed.ac.uk/twiki/bin/view/TWiki/BioKbPlugin as a plugin for the TWiki engine.

Simple namespaces
Extension matrix - source
Widgets (incl. Slideshare)
BibWiki extension — possibly very useful in relation to bibliographic namespace
BibTexImport
Myelink - planned release: end of August 2009
Multi-Category Search, allows for Category intersection, as explained here
SearchLog - logs usage of the search box and allows reporting of keyword totals during given time periods
Labeled Section Transclusion
Assert Edit - useful to limit potential bot damage
Google Wave
Wiki2LaTeX
Google Analytics
Dewikify
ContributionCredits
Extension:FCKeditor (Official) WYSIWYG
Extension:Todo Tasks

Other

typo corrections
git repository for @cz_newdrafts
gitizendium
Wikifind — see http://reid.citizendium.org/bugzilla/show_bug.cgi?id=47#c18
Blinking text
WikiEducator -- nice design of a wiki Welcome page
Zeteo — ζητέω, a database for references, designed for use on Wikipedia
The American encyclopedia of 1851, wikified
A very nice welcome template
HTML color codes and colour slider
Retired Faculty Association at University of Colorado
Association of Retired Faculty at NC State University
animal sounds
Igor - a Google Wave robot to manage your references

rejected Nobel papers

Workgroups

Workgroups are no longer used for group communications, but they still are used to group articles into fields of interest. Each article is assigned to 1-3 Workgroups via the article's Metadata.


Biology article	All articles (1,623)	To Approve (0)	Editors: active (1) / inactive (46) and Authors: active (441) / inactive (0)	Workgroup Discussion
	Recent changes	Citable Articles (25)
		Subgroups (12.5)

Checklist-generated categories:

Underlinked (753)
Cat Check (506)
Cleanup (0)

Subpage categories:

Definitions (1,562)
Related Articles (1,441
to check 710)
Bibliography (400)
External Links (446)
Gallery (30)
Video (33)

Missing subpage categories:

Article statuses:

104 Developed (status=1)
673 Developing (status=2)
699 Stub (status=3)
105 External (status=4)
128 Advanced (status 0-1)
801 Nonstub (status 0-2)
1,500 Internal (status 0-3)

Workgroups are no longer used for group communications, but they still are used to group articles into fields of interest. Each article is assigned to 1-3 Workgroups via the article's Metadata.

Physics Workgroup

Physics article

All articles (884)

To Approve (0)

Editors: active (1) / inactive (24)
and
Authors: active (241) / inactive (0)

Workgroup Discussion

Recent changes

Citable Articles (16)

Subgroups (2.5)

Checklist-generated categories:

Underlinked (315)
Cat Check (224)
Cleanup (0)

Subpage categories:

Definitions (848)
Related Articles (734
to check 319)
Bibliography (194)
External Links (197)
Gallery (5)
Video (17)

Missing subpage categories:

Article statuses:

56 Developed (status=1)
449 Developing (status=2)
363 Stub (status=3)
1 External (status=4)
71 Advanced (status 0-1)
520 Nonstub (status 0-2)
883 Internal (status 0-3)

Workgroups are no longer used for group communications, but they still are used to group articles into fields of interest. Each article is assigned to 1-3 Workgroups via the article's Metadata.

Psychology Workgroup

Psychology article

All articles (263)

To Approve (0)

Editors: active (0) / inactive (28)
and
Authors: active (174) / inactive (0)

Workgroup Discussion

Recent changes

Citable Articles (0)

Subgroups (1)

Checklist-generated categories:

Underlinked (124)
Cat Check (110)
Cleanup (0)

Subpage categories:

Missing subpage categories:

Article statuses:

9 Developed (status=1)
126 Developing (status=2)
123 Stub (status=3)
1 External (status=4)
9 Advanced (status 0-1)
135 Nonstub (status 0-2)
258 Internal (status 0-3)

Workgroup	Total articles	Developed #	Developed %	Approved #	Approved %
Biology	1,623	104	6.4%	25	1.5%
Physics	884	56	6.3%	16	1.8%
Psychology	263	9	3.4%	0	0%
Citizendium project	16,469	1,128	6.8%	0	0%

Interesting research papers

Mühlau, M. (2009), "Voxel-Based Morphometry in Individual Patients: A Pilot Study in Early Huntington Disease", American Journal of Neuroradiology 30 (3): 539-543, DOI:10.3174/ajnr.A1390

add co-authors

Wang, Yue (2007), "Mathematical and Linguistic Processing Differs Between Native and Second Languages: an fMRI Study", Brain Imaging and Behavior 1: 68-82, DOI:10.1007/s11682-007-9007-y

add co-authors

Lüders (2009), "The underlying anatomical correlates of long-term meditation: larger hippocampal and frontal volumes of grey matter", Neuroimage 45: 672, DOI:10.1016/j.neuroimage.2008.12.061

add co-authors

Jäncke, Lutz (2009), "The Architecture of the Golfer's Brain", PLoS ONE 4: e4785, DOI:10.1371/journal.pone.0004785

add co-authors

Endocrine disruptors in bottled mineral water: total estrogenic burden and migration from plastic bottles
Travelling-wave nuclear magnetic resonance
Ryan, M.J. & E.A. Brenowitz (1985), "The Role of Body Size, Phylogeny, and Ambient Noise in the Evolution of Bird Song", American Naturalist 126 (1): 87, DOI:10.1086/284398
Bard, J.B. (2005), "Anatomics: the intersection of anatomy and bioinformatics", J Anat 206 (1): 1–16, DOI:10.1111/j.0021-8782.2005.00376.x
Bard, J. (2007), "Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species.", Mammalian Genome 18 (6): 402–411, DOI:10.1007/s00335-007-9027-3
Doering, J.E.; K. Kane & Y.C. Hsiao et al. (2008), "Species differences in the expression of Ahi1, a protein implicated in the neurodevelopmental disorder Joubert syndrome, with preferential accumulation to stigmoid bodies", The Journal of Comparative Neurology 511 (2): 238–256, DOI:10.1002/cne.21824
Valente, E.M.; F. Brancati & B. Dallapiccola (2008), "Genotypes and phenotypes of Joubert syndrome and related disorders", European Journal of Medical Genetics 51 (1): 1–23, DOI:10.1016/j.ejmg.2007.11.003
Aizenberg, Joanna; James C. Weaver & Monica S. Thanawala et al. (2005), "Skeleton of Euplectella sp.: Structural Hierarchy from the Nanoscale to the Macroscale", Science 309 (5732): 275–278, DOI:10.1126/science.1112255 ^[e]
Bourne, Philip E. & J. Lynn Fink (2008), "I Am Not a Scientist, I Am a Number", PLoS Computational Biology 4: e1000247, DOI:10.1371/journal.pcbi.1000247 ^[e]
Sagotsky, Jonathan A.; Le Zhang & Zhihui Wang et al. (2008), "Life Sciences and the web: a new era for collaboration", Molecular Systems Biology 4 (1): 201, DOI:10.1038/msb.2008.39 ^[e]
Economics needs a scientific revolution
"Mind reading"
Biomineralization organic fossils
cryptobiosis semi-fossil date seed germination
Face processing area macaque brain
Foreign language acquisition in honey bees (OA)
Formants and size perception
Gender differences in breast feeding
Hay fever vaccination
inborn fear system infant emotion (OA)
Jazz music improvisation fMRI (OA)
Mammoth genetics Siberia
Movie blockbuster prediction; popularity; social interaction
seal navigation star
Serotonin hunger aggression
star cult; popularity; media; social interaction; personality
Talheim massacre ancient genetics
Braun, A.R.; McArdle, J.; Jones, J.; Nechaev, V.; Zalewski, C.; Brewer, C.; Drayna, D. (2008). "Tune Deafness: Processing Melodic Errors Outside of Conscious Awareness as Reflected by Components of the Auditory ERP". PLoS ONE 3 (6). DOI:10.1371/journal.pone.0002349. Research Blogging.

Vivipary evolution
whale song; acoustic tracking; humpback whale; Megaptera novaeangliae; sexual selection; social interaction
Sylvester, A.D.; Christensen, A.M.; Kramer, P.A. (2006). "Factors influencing osteological changes in the hands and fingers of rock climbers.". Journal of Anatomy 209 (5): 597. Retrieved on 2008-06-18.

Granot, Y.; Ivorra, A.; Rubinsky, B. (2008). "A New Concept for Medical Imaging Centered on Cellular Phone Technology". PLoS ONE 3 (4). DOI:10.1371/journal.pone.0002075. Research Blogging.

Meyerowitz, E.M. (2002). "Plants Compared to Animals: The Broadest Comparative Study of Development". Science 295 (5559): 1482-1485. DOI:10.1126/science.1066609. Research Blogging.

Jones, D.K. (2004). "The effect of gradient sampling schemes on measures derived from diffusion tensor MRI: A Monte Carlo study". Magnetic Resonance in Medicine 51 (4): 807-815. DOI:10.1002/mrm.20033. Research Blogging.

Tuch, D.S. (2004). "Q-ball imaging.". Magn Reson Med 52 (6): 1358-72. DOI:10.1002/mrm.20279. Research Blogging.

Wedeen, V.J.; Wang, R.P.; Schmahmann, J.D.; Benner, T.; Tseng, W.Y.I.; Dai, G.; Pandya, D.N.; Hagmann, P.; D'arceuil, H.; De Crespigny, A.J. (2008). "Diffusion spectrum magnetic resonance imaging (DSI) tractography of crossing fibers". Neuroimage. DOI:10.1016/j.neuroimage.2008.03.036. Research Blogging.

complementary to deep homology: Insel, T.R. (2006). "From species differences to individual differences". Molecular psychiatry 11 (5): 424. DOI:10.1038/sj.mp.4001826. Research Blogging.

Tuned Responses of Astrocytes and Their Influence on Hemodynamic Signals in the Visual Cortex
Rilling, J.K.; Glasser, M.F.; Preuss, T.M.; Ma, X.; Zhao, T.; Hu, X.; Behrens, T.E. (2008). "The evolution of the arcuate fasciculus revealed with comparative DTI.". Nat Neurosci. DOI:10.1038/nn2072. Research Blogging.

Su, M.Y.; Tapp, P.D.; Vu, L.; Chen, Y.F.; Chu, Y.; Muggenburg, B.; Chiou, J.Y.; Chen, C.; Wang, J.; Bracco, C.; Head, E. (2005). "A longitudinal study of brain morphometrics using serial magnetic resonance imaging analysis in a canine model of aging". Progress in Neuropsychopharmacology & Biological Psychiatry 29 (3): 389-397. DOI:10.1016/j.pnpbp.2004.12.005. Research Blogging.

Flow

Dietrich, A. (2004). "Neurocognitive mechanisms underlying the experience of flow". Consciousness and Cognition 13 (4): 746-761. DOI:10.1016/j.concog.2004.07.002. Research Blogging.

Lee, E. (2005). "The Relationship of Motivation and Flow Experience to Academic Procrastination in University Students". The Journal of Genetic Psychology 166 (1): 5-15.

Rodríguez-sánchez, A.M.; Schaufeli, W.B.; Salanova, M.; Cifre, E. (2008). "Flow experience among information and communication technology users.". Psychol Rep 102 (1): 29-39.

Decety, J.; Jackson, P.L.; Sommerville, J.A.; Chaminade, T.; Meltzoff, A.N. (2004). "The neural bases of cooperation and competition: an fMRI investigation". Neuroimage 23 (2): 744-751. DOI:10.1016/j.neuroimage.2004.05.025. Research Blogging.

Zhai, J.; Barreto, A.B.; Chin, C.; Li, C. (2005). "User stress detection in human-computer interactions.". Biomed Sci Instrum 41: 277-82.

Johnstone, T.; Van Reekum, C.M.; Hird, K.; Kirsner, K.; Scherer, K.R. (2005). "Affective Speech Elicited With a Computer Game.". Emotion 5 (4): 513-518.

Picard, R.W. (2003). "Affective computing: challenges". International Journal of Human-Computer Studies 59 (1-2): 55-64. DOI:10.1016/S1071-5819(03)00052-1. Research Blogging.

Videos to watch

Es gibt im Norden Kolumbiens eine Ecke, die Sierra Nevada, in der ein Indianerstamm lebt, der wohl den letzten verbleibenden Ueberrest der Tairona-Hochkultur nach Ankuft der spanischen Conquistadores darstellt. Die Kogi, wie sie sich nennen, hatten sich in unwirtliches bergiges Gebiet zurueckgezogen, und ueber Jahrhunderte hinweg jeglichen Kontakt mit uns gemieden, weil sie die schmerzhafte Erfahrung gemacht hatten, dass die Beruehrung mit dem, was wir "Zivilisation" nennen, unvermeidlich immense zerstoererische Prozesse in Gang setzt.

Vor knapp 20 Jahren, im Jahr 1990, hatten die Kogi einen "von uns" zu sich geholt, um uns, die sie als "younger brother" bezeichnen, eine Botschaft zu uebermitteln: Alan Ereira von der BBC, der den Film "A message from the heart of the world" ueber die Kogi gedreht hatte.

Die Kernbotschaft ist: In der Sierra Nevada, einer der Biodiversitaets-Hotspots des Planeten, vollziehen sich besorgniserregende Veraenderungen in der Biologie, die einem aufmerksamen Beobachter auffallen, und nur die Interpretation zulassen, dass aehnliche Prozesse auf der ganzen Welt ablaufen muessen. Das hat die Kogi dazu veranlasst, die - in ihrer Wahrnehmung immense - Gefahr auf sich zu nehmen, aus ihrer Isolation herauszukommen, weil sie sehen, dass die ganze Welt dabei ist, ins Chaos zu taumeln.

The structure of social collaboration on Wikipedia
Wikipedia’s Labor Squeeze and its Consequences by Eric Goldman

context

recommended:

Practical Semantic Web and Why You Should Care - Boris Mann

OpenID, Drupal, and the Open Web - James Walker

Keynote: Is Drupal Moral? - David Weinberger

Scaling Drupal: Not IF...HOW - Thomas Wysocki

Drupal Multimedia - Aaron Winborn

Building Advanced Social Networks at a Large U.S. University - Kyle Mathews

Watched

TED talk: Ken Robinson says schools kill creativity — great! Details here
James Lovelock about long-term perspectives for human society on our planet
A World Without Water - comment here
insect flight patterns

Craig Venter on synthetic genomics

puts the Origin of species at 1879 but otherwise, it's fascinating.

brief overview of history of gene sequencing

Google Wave announcement

Announcement of a new internet protocol that may turn out to be very interesting in a scientific context

Tim Berners-Lee: The next Web of open, linked data

a shout-out for "Raw Data Now", nice intro for those who never heard of Open Data initiatives before

Need a little validation?

about the power of being nice; too long for my taste (I stopped after 5:34 min)

Featured images

http://commons.wikimedia.org/wiki/File:Auf_dem_Valar-Karpaten1978.jpg

Get current source

I sometimes take a CZ article home to work on it offline. Candidates for this are:

Orphaned subpages

Self-replication: Add brief definition or description
Skeleton: Add brief definition or description
Christiansen, P. (2001), "Mass allometry of the appendicular skeleton in terrestrial mammals", J. Morphol. 251: 195–209, DOI:10.1002/jmor.1083 ^[e]
Environment (biology): Add brief definition or description
Cerebellum: Add brief definition or description
Computational_biology: Add brief definition or description
Talk by Gary Bader on "Current Issues in Computational Biology and Bioinformatics"

Single-nucleotide_polymorphism: Add brief definition or description
Whistling: Add brief definition or description
Wich, Serge A.; Karyl B. Swartz & Madeleine E. Hardus et al. (2009), "A case of spontaneous acquisition of a human sound by an orangutan", Primates: in press, DOI:10.1007/s10329-008-0117-y ^[e]
Transcranial_magnetic_stimulation: Add brief definition or description
Hallett, M. (2007), "Transcranial Magnetic Stimulation: A Primer", Neuron 55 (2): 187–199, DOI:10.1016/j.neuron.2007.06.026 ^[e]

Offline notes

Move this to Topics??

This section contains notes made about (or passages copied from, often with considerable losses in formatting, particularly concerning equations and special characters) books or papers I read offline. I plan to incorporate these points, as time permits, into current or future CZ articles. In practice, this probably won't happen in areas too far off my core topics (see above) but if you are knowledgeable about any of these subjects, I would appreciate if you would provide additional information, references or comments, be it via the corresponding CZ article (which, if it exists, should provide some useful context), this page or email.

Abstract (publishing)

Abstract (publishing) [r]: Add brief definition or description

A longer one: ""Chronoastrobiology: are we at the threshold of a new science? Is there a critical mass for scientific research?" A simple photograph of the planet earth from outer space was one of the greatest contributions of space exploration. It drove home in a glance that human survival depends upon the wobbly dynamics in a thin and fragile skin of water and gas that covers a small globe in a mostly cold and vast universe. This image raised the stakes in understanding our place in that universe, in finding out where we came from and in choosing a path for survival. Since that landmark photograph was taken, new astronomical and biomedical information and growing computer power have been revealing that organic life, including human life, is and has been connected to invisible (non-photic) forces, in that vast universe in some surprising ways. Every cell in our body is bathed in an external and internal environment of fluctuating magnetism. It is becoming clear that the fluctuations are primarily caused by an intimate and systematic interplay between forces within the bowels of the earth--which the great physician and father of magnetism William Gilbert called a 'small magnet'--and the thermonuclear turbulence within the sun, an enormously larger magnet than the earth, acting upon organisms, which are minuscule magnets. It follows and is also increasingly apparent that these external fluctuations in magnetic fields can affect virtually every circuit in the biological machinery to a lesser or greater degree, depending both on the particular biological system and on the particular properties of the magnetic fluctuations. The development of high technology instruments and computer power, already used to visualize the human heart and brain, is furthermore making it obvious that there is a statistically predictable time structure to the fluctuations in the sun's thermonuclear turbulence and thus to its magnetic interactions with the earth's own magnetic field and hence a time structure to the magnetic fields in organisms. Likewise in humans, and in at least those other species that have been studied, computer power has enabled us to discover statistically defined endogenous physiological rhythms and further direct effects that are associated with these invisible geo- and heliomagnetic cycles. Thus, what once might have been dismissed as noise in both magnetic and physiological data does in fact have structure. And we may be at the threshold of understanding the biological and medical meaning and consequences of these patterns and biological-astronomical linkages as well. Structures in time are called chronomes; their mapping in us and around us is called chronomics. The scientific study of chronomes is chronobiology. And the scientific study of all aspects of biology related to the cosmos has been called astrobiology. Hence we may dub the new study of time structures in biology with regard to influences from cosmo- helio- and geomagnetic rhythms chronoastrobiology. It has, of course, been understood for centuries that the movements of the earth in relation to the sun produce seasonal and daily cycles in light energy and that these have had profound effects on the evolution of life. It is now emerging that rhythmic events generated from within the sun itself, as a large turbulent magnet in its own right, can have direct effects upon life on earth. Moreover, comparative studies of diverse species indicate that there have also been ancient evolutionary effects shaping the endogenous chronomic physiological characteristics of life. Thus the rhythms of the sun can affect us not only directly, but also indirectly through the chronomic patterns that solar magnetic rhythms have created within our physiology in the remote past. For example, we can document the direct exogenous effects of given specific solar wind events upon human blood pressure and heart rate. We also have evidence of endogenous internal rhythms in blood pressure and heart rate that are close to but not identical to the period length of rhythms in the solar wind. These were installed genetically by natural selection at some time in the distant geological past. This interpretive model of the data makes the prediction that the internal and external influences on heart rate and blood pressure can reinforce or cancel each other out at different times. A study of extensive clinical and physiological data shows that the interpretive model is robust and that internal and external effects are indeed augmentative at a statistically significant level. Chronoastrobiological studies are contributing to basic science--that is, our understanding is being expanded as we recognize heretofore unelaborated linkages of life to the complex dynamics of the sun, and even to heretofore unelaborated evolutionary phenomena. Once, one might have thought of solar storms as mere transient 'perturbations' to biology, with no lasting importance. Now we are on the brink of understanding that solar turbulences have played a role in shaping endogenous physiological chronomes. There is even documentation for correlations between solar magnetic cycles and psychological swings, eras of belligerence and of certain expressions of sacred or religious feelings. Chronoastrobiology can surely contribute to practical applications as well as to basic science. It can help develop refinements in our ability to live safely in outer space, where for example at the distance of the moon the magnetic influences of the sun will have an effect upon humans unshielded by the earth's native magnetic field. We should be better able to understand these influences as physiological and mechanical challenges, and to improve our estimations of the effects of exposure. Chronoastrobiology moreover holds great promise in broadening our perspectives and powers in medicine and public health right here upon the surface of the earth. Even the potential relevance of chronoastrobiology for practical environmental and agricultural challenges cannot be ruled out at this early stage in our understanding of the apparently ubiquitous effects of magnetism and hence perhaps of solar magnetism on life. The evidence already mentioned that fluctuations in solar magnetism can influence gross clinical phenomena such as rates of strokes and heart attacks, and related cardiovascular variables such as blood pressure and heart rate, should illustrate the point that the door is open to broad studies of clinical implications. The medical value of better understanding magnetic fluctuations as sources of variability in human physiology falls into several categories: 1) The design of improved analytical and experimental controls in medical research. Epidemiological analyses require that the multiple sources causing variability in physiological functions and clinical phenomena be identified and understood as thoroughly as possible, in order to estimate systematic alterations of any one variable. 2) Preventive medicine and the individual patients'care. There are no flat 'baselines', only reference chronomes. Magnetic fluctuations can be shown statistically to exacerbate health problems in some cases. The next step should be to determine whether vulnerable individuals can be identified by individual monitoring. Such vulnerable patients may then discover that they have the option to avoid circumstances associated with anxiety during solar storms, and/or pay special attention to their medication or other treatments. Prehabilitation by self-help can hopefully complement and eventually replace much costly rehabilitation. 3) Basic understanding of human physiological mechanisms. The chronomic organization of physiology implies a much more subtle dynamic integration of functions than is generally appreciated. All three categories of medical value in turn pertain to the challenges for space science of exploring and colonizing the solar system. The earth's native magnetic field acts like an enormous umbrella that offers considerable protection on the surface from harsh solar winds of charged particles and magnetic fluxes. The umbrella becomes weaker with distance from the earth and will offer little protection for humans, other animals, and plants in colonies on the surface of the moon or beyond. Thus it is important before more distant colonization is planned or implemented to better understand those magnetism-related biological- solar interactions that now can be studied conveniently on earth. Thorough lifelong maps of chronomes should be generated and made available to the scientific world. Individual workers should not have to rediscover cycles and rhythms, which can be a confusing source of variation when ignored. By contrast, once mapped, the endpoints of a spectral element in chronomes can serve everybody, for instance for the detection of an elevation of vascular disease risk. Chronomic cartography from birth to death is a task for governments to implement, thereby serving the interests of transdisciplinary science and the general public alike. Governments have supported the systematic gathering of physical data for nearly two centuries on earth in order to serve exploration, trade, and battle on land and on the seas, and indeed agriculture. These government functions have been augmented enormously with satellite technology in more recent decades. The biological comparison with regard to government support and chronomic needs would be the mapping of the human genome. The complete sequences of DNA might have eventually become available due simply to countless individual laboratories publishing piecemeal results in scattered journals. But there would have been enormous redundancy and confusion in assembling and piecing the information together. The waste of time and money involved in the redundancy and confusion would have been considerable. (ABSTRACT TRUNCATED)"

Animal

Animal [r]: Add brief definition or description
add section on fossils
the probably oldest animal remains known today are demosponge steranes aged over 635 million years (cf. Fossil steroids record the appearance of Demospongiae during the Cryogenian period)
animal sounds

Arctic

Arctic [r]: Add brief definition or description

CLIMATE OF THE ARCTIC MARINE ENVIRONMENT

Arnold Dohmen

Arnold Dohmen [r]: Add brief definition or description

Arnold Dohmen (born August 2, 1906 in Buchholz/Duisburg, Germany), was a German physician specialized in internal medicine and bacteriology who performed human experimentation in Nazi concentration camps.

Internist und klinische Bakteriologe Arnold Dohmen (geb. 2.8.1906 in Buchholz/Duisburg) gehörte bei Kriegsbeginn zur Medizinischen Klinik von Prof. H.H. Berg in Hamburg Eppendorf, wo er bis Ende des Krieges blieb. Ab Mai 1940 nahm er am "Frankreichfeldzug" teil, er gehörte zur 20. Division (mot.), 1. San. Kompanie. Hier führte er in St. Honoré eine erste Untersuchung über eine Gelbsuchtepidemie durch, die später im Deutschen Militärarzt publiziert wurde. Im Nov. 1940 wurde er nach Hamburg zurückversetzt, um dort seine Habil. Zum Thema Weilsche Krankheit (Spirochäten-Infektion) zu Ende zu bringen (Aussprache 19.2.1941). Anfang April 1941 wurde er noch einmal nach Frankreich eingezogen, wo er u.a. Untersuchungen am Institut Pasteur durchführte.

A personal account of these experiments is given (in German) by Saül Oren-Hornfeld, one of Dohmen's subjects, in Geschichte der Kaiser-Wilhelm-Gesellschaft im Nationalsozialismus (pp. 94-101) and (in French) in Oren-Hornfeld's autobiography, Comme un feu brûlant.

Astrolabe

Astrolabe [r]: Add brief definition or description
Tom Wujec demos the 13th-century astrolabe

Aurora borealis

Bagel

Bagel [r]: Add brief definition or description

Mathematically Correct Breakfast — How to Slice a Bagel into Two Linked Halves

Bionics

Billion

Billion [r]: Add brief definition or description

a blog post about the concept

Quotes:

"One billion minutes ago, around 100 C.E., Greek mathematician Ptolemy was being born, the wheelbarrow had just been invented in China, the last lions in the Balkan Peninsula were dying off, the Kama Sutra was starting to have its first pages written in India, bricks were the new trend in Roman housing development and, again in China, paper was thought of being a pretty neat new idea."
"One billion hours ago Australia was not inhabitated by humans and there was no agriculture and no domesticated animals. We were all basically living in Africa, chipping stones to slice meat off bones and fashion animal hide into early-days togas for our northbound walks into cold places. We would answer to erectus rather than sapiens and were just starting to develop language and music."

Biomechanics

Biomechanics [r]: Add brief definition or description

Gordon_2006_Mechanics_in_embryogenesis_and_embryonics_prime_mover_or_epiphenomenon.pdf

Blind spot

Blind spot [r]: Add brief definition or description
great demonstration via Vanishing Head Illusion

Brain development

Brain development [r]: Add brief definition or description

add barcroft 1942

and Johnson 2005 Processes of change in brain and cognitive development.pdf

Faulkner 2007 Axon Pruning in the Developing Vertebrate Hippocampus

Keller_2006_Resolving the paradox of common harmful heritable mental disorders

add mattick 2008

O'Leary 2007

COUP-TFI, Emx2, Pax6, and Sp8,

Rebsam 2008/ Sugiyama 2008

Otx2

Levitt, P. (2003) Structural and functional maturation of the developing primate brain. J. Pediatr., 143 (Suppl. 4), S35S45.

Agarwala, S., Sanders, T.A. and Ragsdale, C.W. (2001) Sonic hedgehog control of size and shape in midbrain pattern formation. Science, 291, 21472150.

add Meyer 2000 Embryonic and Early Fetal Development of the Human Neocortex

Brain evolution

Brain evolution [r]: Add brief definition or description

Keller_2006_Resolving the paradox of common harmful heritable mental disorders

Farris SM (2008) Evolutionary convergence of higher brain centers spanning the protostome-deuterostome boundary. Brain Behav Evol 72:106122.

--> get it!

Levitt, P. (2003) Structural and functional maturation of the developing primate brain. J. Pediatr., 143 (Suppl. 4), S35S45.

Brain function

Brain function [r]: Add brief definition or description

Thaut, M.H.; Demartin, M.; Sanes, J.N. (2008). "Brain Networks for Integrative Rhythm Formation". PLoS ONE 3 (5). DOI:10.1371/journal.pone.0002312. Research Blogging.

Stevens, L.T. (1886). "On the time sense". Mind 11 (43): 393-404.

Brain morphometry

Brain morphometry [r]: Add brief definition or description

Surfaces and Flat Maps

Burish_2004_brain_morphology_social_complexity_birds.pdf

cytoarchitectonic areas

Lefebvre 2008:

"Unfortunately, brain imaging studies are usually conducted on single species and almost never compare animals that show lifestyle differences likely to affect cognition. A remarkable exception is the work of Goodson and co-authors on the neural basis of avian sociality. The work from this group uses state-of-the-art neuroscience techniques to, among other things, map the receptor density

of neuropeptides involved in sociality; the sample of species is remarkably broad for this kind of study (five), and the authors distinguish cases of independent and phylogenetically-correlated evolution. The studies identify neurohormone receptor site differences that correlate with sociality differences in 13 different brain centers ranging from the sub-pallial septum to the stria terminalis,

the hypothalamus and the hippocampus [see table 1 in Goodson et al., 2006]."

and

"It would be interesting if Goodsons comparative research program on sociality and fine level neuronal measures could address the assumptions of brain size research, for example by looking at the relationship between neuropeptide receptor density and size of structures involved in sociality such as the amygdala, the septal complex, the hypothalamus and the hippocampus."

Goodson JL, Evans AK, Wang Y (2006) Neuropeptide binding reflects convergent and divergent evolution in species-typical group sizes. Horm Behav 50: 223236.

tensor-based morphometry in schizophrenia: Gogtay 2008 --> how are their deformation fields computed?

cross 2008 Age-related decrease in axonal transport measured

van Haren 2008 Genes and structural brain imaging in schizophrenia

"There is sufficient evidence to defend the use of structural neuroimaging as an endophenotype to investigate a complex phenotype such as schizophrenia despite the

notion that, so far, no single causal pathway emerges from these studies."

on microscopy in general: e.g. liem 2008 in farmer 2008: motoneuron GFP

2005_Corruccini_1987_comparative_morphology_evolution_allometry.pdf

Andreasen, N. C., Arndt, S., Swayze, V., 2nd, Cizadlo, T., Flaum, M., O'Leary, D., Ehrhardt, J. C., and Yuh, W. T. 1994. Thalamic abnormalities in schizophrenia visualized through magnetic resonance image averaging. Science 266: 294–298.

one of the earliest studies using VBM

Chung, M.K., Worsley, K.J., Paus, T., Cherif, C., et al., 2001. A unified statistical approach to deformation-based morphometry. NeuroImage 14(3), 595–606.

Johnson, G.A., Cofer, G.P., Fubrara, B., Gewalt, S.L., Hedlund, L.W., Maronpot, R.R., 2002. Magnetic resonance histology for morphologic phenotyping. J. Magn. Reson. Imaging 16, 423–429.

check for neuroimaging in there

Ashburner, J., Hutton, C., Frackowiak, R., Johnsrude, I., Price, C., Friston, K., 1998. Identifying global anatomical differences: deformation-based morphometry. Hum. Brain Mapp. 6, 348–357.

Brain plasticity

Brain plasticity [r]: Add brief definition or description

Smirnakis, S. M., Brewer, A. A., Schmid, M. C., Tolias, A. S., Schuz, A., Augath, M., et al. (2005). Lack of

long-term cortical reorganization after macaque retinal lesions. Nature, 435(7040), 300307.

Reports on limits to brain plasticity.

See also Ramus 2006: "Ironically, plasticity is among the properties of the brain that must be under

the tightest genetic control. Indeed, the molecular mechanisms that modulate

neurons response to activity and changes thereof are precisely the sort of

processes that genes trigger and regulate."

Seri 2001: Astrocytes give rise to neurons in the adult mammalian hippocampus

Rebsam 2008: Otx2s Incredible Journey

-"visual experience triggers cellto-

cell transfer of the homeoprotein Otx2 to cortical interneurons, where it promotes maturation of

inhibitory neural circuitry and opens the critical period for plasticity in the visual cortex"

Brain size

Brain size [r]: Add brief definition or description

check p. 781 in Götz 2005 in ASPM and microcephaly

Byrne 2007:

"In

a natural experiment, the cranial fossils of a Majorcan

bovid showed a striking drop in brain size after its

only mammalian predator died out (Figure 3) [50]."

Köhler, M., and Moya-Sola, S. (2004). Reduction of brain and sense organs in the fossil insular bovid Myotragus. Brain Behav. Evol. 63, 125140.

Chaos

Chaos [r]: Add brief definition or description

illustration

Charles Bonnett syndrome

Cleavage plane orientation

Cleavage plane orientation [r]: Add brief definition or description

Here, I have unpublished data (obtained together with Jörg Jakobi and Hans-Peter Richter) on the effect of magnetic field strength on third cleavage orientation in Xenopus laevis, contradicting earlier studies by Denegre, Valles et al. (1998 onwards). If you are interested in details, just drop me a line.

Götz 2005 the cell biology of neurogenesis

cites Chenn 1995 on cleavage orientation and asymmetric cell division

Cluster analysis

Colour blindness

Comparative biology

Comparative biology [r]: Add brief definition or description

with redirect from Comparative method

Diogo R, Abdala V, Lonergan N, Wood BA (2008). "From fish to modern humans--comparative anatomy, homologies and evolution of the head and neck musculature.". J Anat 213 (4): 391-424. DOI:10.1111/j.1469-7580.2008.00953.x. PMID 18657257. Research Blogging.

also relevant for homology, vertebrate and possibly evolution

Sherry. NEUROECOLOGY. Annu. Rev. Psychol. 2006. 57:16797

Rehkämper 1991

Lefebvre 2008:

"Unfortunately, brain imaging studies are usually conducted on single species and almost never compare animals that show lifestyle differences likely to affect cognition. A remarkable exception is the work of Goodson and co-authors on the neural basis of avian sociality. The work from this group uses state-of-the-art neuroscience techniques to, among other things, map the receptor density

of neuropeptides involved in sociality; the sample of species is remarkably broad for this kind of study (five), and the authors distinguish cases of independent and phylogenetically-correlated evolution. The studies identify neurohormone receptor site differences that correlate with sociality differences in 13 different brain centers ranging from the sub-pallial septum to the stria terminalis,

the hypothalamus and the hippocampus [see table 1 in Goodson et al., 2006]."

and

"It would be interesting if Goodsons comparative research program on sociality and fine level neuronal measures could address the assumptions of brain size research, for example by looking at the relationship between neuropeptide receptor density and size of structures involved in sociality such as the amygdala, the septal complex, the hypothalamus and the hippocampus."

Goodson JL, Evans AK, Wang Y (2006) Neuropeptide binding reflects convergent and divergent evolution in species-typical group sizes. Horm Behav 50: 223236.

Cordyceps

Cryobiology

Cryobiology [r]: Add brief definition or description

http://en.wikipedia.org/wiki/Insect_winter_ecology

Cryptobiosis

Cryptobiosis [r]: Add brief definition or description

Clegg, J.S. (2001), "Cryptobiosis — a peculiar state of biological organization", Comparative Biochemistry and Physiology, Part B 128 (4): 613–624

Biorisk project using bloodworms in space

Deep homology

Deep homology [r]: Add brief definition or description

Elman, J. L., Bates, E. A., Johnson, M. H., KarmiloV-Smith, A., Parisi, D., & Plunkett, K. (1996). Rethinking

innateness: A connectionist perspective on development. Cambridge, MA: MIT Press.

King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107116.

cited by Carroll 2005

Minelli

From Minelli 2003: The Development of Animal Form chap 10:Evo-devo perspectives on homology (p. 222-249) p. 251 (summary):"homology is a relative, rather than an absolute concept."

Buss 1987 The Evolution of Individuality

developmental role for cilia; mitosis in metazoan cells is blocked once they have cilia

Jacob, J.; A. Hacker & S. Guthrie (2001), "Mechanisms and molecules in motor neuron specification and axon pathfinding", BioEssays 23 (7): 582–595, DOI:10.1002/bies.1084
Arnone, Davidson 1997: The hardwiring of development: organization and function of genomic regulatory systems
Arthur 2002: The emerging conceptual framework of evolutionary developmental biology
Shubin, Wake 1996: Phylogeny, variation, and morphological integration
Wolpert-L: several papers on "positional information"

also (1994) "The evolutionary origin of development"

and (1998) debatable issues

what is conserved in evolution: the operation!

Wake 1991: Homoplasy: The result of natural selection or evidence of design limitation?

see also Wake 1999 in Homology (Novartis Foundation Symposium 222)

Reeck 1987: Homology in proteins and nucleic acids
Müller, Newman 1999 in Homology (Novartis Foundation Symposium 222)
Raff 1998 cell number control and timing
Egel 2000: how homology entered genetics
Gubb 1998: cellular polarity ... growth ... information
Hanken, Wake 1993: Miniaturization of body size
Morata, Sanchez-Herrero 1999:Patterning mechanisms in the body trunk

shows that (at least some) morphological boundaries coincide with boundaries in gene expression

Abzhanov, Popadic, Kaufman 1999: chelicerate hox genes and the homology of arthropod segments
Gilbert, Bolker 2001: homology of process

scope of homology, with focus on genes

Galis 1996:The evolution of insects and vertebrates: homeobox genes and homology

2001:Why five fingers?

p. 231:"Consideration of the whole developmental pathway is required for a sensible assessment of homology. To take the whole developmental pathway into account, it is not enough to consider the expression patterns of more than one gene and the control cascades in which these genes are involved. it is necessary to study, in addition, the epigenetic properties of development (Müller and Newman, 1999), that is, the generic properties of molecules, cells and tissues, and the interaction dynamics among them."

Greenspan 2001: The flexible genome

posits that degeneracy, not redundancy, explains why some k.o. mice do not seem to have phenotypic effects

"An interesting difference between redundant systems and degenerate systems is that the former are likely to produce clearly identifiable homologues, whereas the latter are likely to be features with complex and perhaps contradictory homologous components."

Newman and Müller 2000:Epigenetic mechanisms of character origination

regard epigenetics as crucial for morphological innovations

p. 234:"Definitely, the single most important requirement, when addressing a problem of homology, is probably the identification of meaningful units to be compared. Until recently, virtually all assessments of homology involved morphological units, either in adults or earlier developmental stages. New perspectives were explored by the recent turn towards developmentally defined morphological units (e.g., Wagner 1989, Schwenk 2001) and processes (e.g., Butler and Saidel 2000, Gilbert and Bolker 2001)." Wagner 1989: The biological homology concept Butler, Saidel 2000: Defining sameness

Israelsson 1999: New light on th enigmatic Xenoturbella (phylum unknown)

p. 234: "To describe any of those parts of the phenotype which behave as a relatively independent functionally integrated group of traits, Wagner introduced the concept of module (Wagner 1996, Wagner and Altenberg 1996). A module produces an integrated character complex and is thus both a developmental and an evolutionary unit."

Hernandorena and Marco 1991: heat-induced developmental uncoupling of mesoderm from ectoderm and endoderm germ layer derivatives

p. 237: "are the ectoderm, endoderm and (where present) mesoderm homologous throughout the animal kingdom? Are there animals with more than three germ layers?"

Hall 1998b:germ layers and the germ-layer theory revisited

"In Drosophila, mitotic domain boundaries are cell fate boundaries (Cambridge et al., 1997)."

p. 238: "Nomenclature not withstanding, there is no clear-cut difference between the three traditional germ layers, the neural crest of the vertebrates, the imaginal discs of the holometabolous insects, and the set-aside cells from which the adult will develop in marine invertebrates (such as nemerteans and sea urchins)."

Hall 1998b: set-aside layers = secondary germ layers

but see Henry, Martindale 1998: Evolution of cleavage programs

"Brian Hall (...) has strongly argued in favour of treating the neural crest as a fourth germ layer. The neural crest has been defined as the quintessential feature of vertebrates (...), one of the main keys to their extraordinary adaptive success. In fact, the neural crest parallels. In fact, the neural crest parallels the mesoderm as a major source of internal structures, tissues and organs. Its peculiar 'strategy' is the targeted migratory behaviour of its multiple components."

p. 241:"A field is a group of cells provided with self-organising and self-regulating properties (Ingham and Martínez-Arias 1992).""...if a species can be defined in terms of a shared gene pool, a field can be diefeines in terms of shared gene expression. A morphogenetic field is possibly the lowest term in a whole hierarchy of systems in which evolutionary novelties may arise. This happens following quantitative and qualitative changes in one or more gene expression patterns (Gilbert et al., 1996)."

Gilbert et al., 1996: Resynthesizing evolutionary and developmental biology

see also progenitor field (Davidson 1993) and equivalence group (Horvitz and Sternberg 1991), gene expression territories and compartments

p. 252:"Animal evolution has explored many more solutions than the chicken, mouse, zebrafish, Drosophila, and Caenorhabditis would suggest. [...] Wide-ranging comparisons and a combined interdisciplinary approach are required before evolutionary biology may finally be written from 'first principles'."

Dionaea muscipula

Dodo

Embryo

Embryo [r]: Add brief definition or description

http://www.flickr.com/photos/euthman/304334264/

Emotion

Emotion [r]: Add brief definition or description

From Ramus 2006:

"James Blair, reviewing extensive data from developmental psychopathy, upgrades

his former Violence Inhibition Model to the Integrated Emotions Systems. In so

doing, he provides extremely speciWc hypotheses (and a wealth of data) on how

genetic anomalies, aVecting a speciWc part of the emotion system, may alter its development

and lead to a relatively speciWc cognitive disorder. Although the genetics of

psychopathy remains to be researched, the neuro-cognitive part of the model is

remarkably well speciWed, so much so that it appears to be the first model of a specific

cognitive developmental disorder that is ready for full integration with biological

detail at the molecular level."

Encephalization

Encephalization [r]: Add brief definition or description

Rehkämper 1991:

"Annelids, arthropods (especially insects)

and mollusks (especially octopods) are well known

to be highly encephalized (Bullock and Horridge 1965;

Young 1971; Maddock and Young 1987). A brain part

is found in all these groups that is organized in the same

way as the vertebrate integrational areas. In annelids,

it is their "midbrain" with the corpora pedunculata.

In insects and chelicerates, this part is the protocerebrum

(corpora pedunculata, protocerebral bridge, central

body), which is interconnected with all other brain parts.

It modulates indirectly the motor output. In octopods,

it is the vertical lobe that is organized as an integrational

centre. It has been proven that the vertical lobe is involved

in complex behaviour and learning (Wells 1978).

All these vertebrate and non-vertebrate groups are

highly encephalized and dominating elements in the recent

fauna. Thus, it can be assumed that the recent fauna

in general is strongly influenced by the biological advantage

of developing multimodal integrational capacities."

Epigenetics

Epigenetics [r]: Add brief definition or description

Arai 2009 Transgenerational Rescue of a Genetic Defect in Long-Term

Potentiation and Memory Formation by Juvenile Enrichment

Erwin Neher

Evolution

The basic method of science after Einstein seems to be: identify something in your theory that is playing the role of an absolute background, that is needed to define the laws that govern objects in your theory, and understand it more deeply as a contingent property, which itself evolves subject to law.
For example, before Einstein the geometry of space was thought of as specified absolutely as part of the laws of nature. After Einstein we understand geometry is contingent and dynamical, which means it evolves subject to law. This means that Einstein's move can even be applied to aspects of what were thought to be the laws of nature: so that even aspects of the laws turn out to evolve in time.
The basic method of science after Darwin seems to be to identify some property once thought to be absolute and defined a prior and recognize that it can be understood because it has evolved by a process of or akin to natural selection. This has revolutionized biology and is in the process of doing the same to the social sciences.
We can see by how I have stated it that these two methods are closely related. Einstein emphasizes the relational aspect of all properties described by science, while Darwin proposes that ultimately, the law which governs the evolution of everything else, including perhaps what were once seen to be laws-is natural selection.
Should Darwin's method be applied even to the laws of physics? Recent developments in elementary particle physics give us little alternative if we are to have a rational understanding of the laws that govern our universe. I am referring here to the realization that string theory gives us, not a unique set of particles and forces, but an infinite list out of which one came to be selected for our universe. We physicists have now to understand Darwin's lesson: the only way to understand how one out of a vast number of choices was made, which favors improbably structure, is that it is the result of evolution by natural selection.

Expertise

Expertise [r]: Add brief definition or description

Some notes on Larry Sanger's essay "The Fate of Expertise After Wikipedia" (Episteme 2009, ###add issue no. + online link### ):

Larry mentions that Wikipedia exists in over 200 languages but most if not all his remarks are made with respect to the English Wikipedia and not necessarily applicable to other language versions

"The topic is well focused by this paradox: are experts still needed when Wikipedia has succeeded, apparently, without them? I think they are; my aim in this paper is to reduce the sense of paradox."

This reminds me of the plot typical for Hollywood movies: Create an artificial problem and spend the rest of the time solving it. Larry's paradox above rests entirely on the ambiguity of what the reader may understand under "without them". If Larry had used a more precise phrasing, the resolution of the paradox would probably have been very easily visible (and his article shorter). To put it in different words:

Are vitamines still needed when mankind has succeeded, apparently, without them?

can be understood as, e.g.,

Are vitamines still needed when mankind has succeeded, apparently, without being able to synthesize them?

or

Are vitamines still needed when mankind has succeeded, apparently, without ingesting them?

The former "apparentness" appears to me to be clearly more "apparent" than the latter. In the Wikipedia context, the vitamines would be pieces of knowledge (similar to what Google dubbed knols) which have to be "ingested" by the project, i.e. entered by some sort of experts, and collaboratively rephrased. Given the wide range of topics covered at Wikipedia, expertise will have to be understood in terms of these subjects (and gradients in expertise - beyond "know-nothings" and "know-somethings", as Larry put it - should be kept in mind): Frequent watchers of some TV series may be regarded as experts in sitcomology, while homeless people, should they be connected to the internet and edit Wikipedia, could certainly contribute expert knowledge on street life and related articles, whereas many who worked professionally on a topic (including having studied it academically) would probably meet the criteria of more traditional definitions of expertise.

The important thing is that most of the knowledge entered into Wikipedia (with the exception of the WP name space and thelike) is acquired outside Wikipedia, just like vitamines are being synthesized outside our bodies. Wikipedia and our bodies are thus open systems, permitting the exchange of information, matter (and heat) with their respective environments. Consequently, the fate of Wikipedia will certainly depend on the regular availability of expert attention (which is a scarce resource in many fields), rather independent of the precise internal rules.

The article contains no figures (or equations, for that matter) but lots of footnotes (not even clickable), making it tedious for me to digest it (my field is neuroimaging, and I have developed the habit to look at the figures and equations first before deciding whether to dive deeper into an article).

Example:

(p. 61) "Imagine a database of research in which new findings are not published in papers that are put into volumes, but appended in various places to a single, collaboratively-managed outline of knowledge."22

(Footnotes section, p. 72) 22 I am far from being the only one to have suggested this, but I developed the idea at some length in my (2006a).

(Reference section, p. 70) Sanger, Larry. 2006a. “Text and Collaboration: A PersonalManifesto for the Text Outline Project.” Posted April 2006. http://www.textop.org/TextAndCollaboration.html

"In physics, for example, there is simply less to debate about than in, say, philosophy."

I object to the "simply less": The difference is not in the amount of things to debate about but in the way of debating - argumentation in physics ultimately boils down to replicable quantification - by measurement, calculation or a combination or (quantitative) critique thereof. This aspect of replicable quantification seems to be much less prominent in philosophy, leaving room for qualitative debates and thereby creating an illusion that there is more to debate in philosophy than elsewhere.

Larry talks about "a vector toward continual improvement", "asymptotically approaching a perfect model of expert opinion" and states

"Over the long term, the quality of a given Wikipedia article will do a random walk around the highest level of quality permitted by the most persistent and aggressive people who follow an article."

What about some quantitative model of the information contents in encyclopedic projects with the boundary conditions provided by the rules in place at Wikipedia, Citizendium or the Encyclopaedia Britannica?

a little later:

"Since experts tend to be very busy professionals, they often cannot keep up their side of the edit war, and they lose by default."

What about the proposal of just requiring editors (in the CZ sense, i.e. subject experts), not _all users_, to use real names, then? Well, experts are less likely to be willing to review anonymous contributions than those filed under a real name.

Fetus

Paul Feyerabend|Feyerabend, Paul

Feyerabend, Paul [r]: Add brief definition or description

http://plato.stanford.edu/entries/feyerabend/

Fractal dimension

Gyrification

Gyrification [r]: Add brief definition or description

micropolygyria (Toda 1999)

Duncan and Olson 1993:

"The shape index and the curvedness are two

properties derived from the principal curvatures that

are also useful.The shape index S is a generalized

measure of concavity and convexity defined by

(3)"

from lockwood 1999:

"Zilles et al. (1989) used a gyrification index to express degrees of convolution in surface area. Measured from cross sections, the index is the length of the complete contour of the surface area divided by the length of the outer contour alone. The expectation is that the gyrification index should increase with larger brain sizes, and Zilles et al. (1989) confirm that this is the case for

primates. However, what is most important about this study is the difference in regression lines between anthropoids and prosimians.

The slope is 0.66 for anthropoids and 0.23 for prosimians, indicating that for every unit increase in brain size, anthropoids acquire a higher degree of cortical folding than do prosimians (Zilles et al., 1989, p. 146).

This example highlights two important aspects of homoplasy. On the one hand, the underlying relationship between convolutions of the brains surface area and total brain size gives rise to potential homoplasy, as parallel increases or reductions in brain size will usually occur with shifts in sulcal development. Zilles et al. (1989) note, for example, that the similar degrees of gyrification in callitrichids and prosimians represents convergent evolution as a side effect of small brain size. This relationship would presumably affect the use of individual sulci as phylogenetic characters. Diagnostic sulci of a particular group will not be present in members with small brains, and if small brains are the primitive condition, this situation could be especially confusing. In the terminology used above in definitions of homoplasy, the relationship between surface convolutions and brain size represents a structural or functional constraint on brain organization that governs the phenotypic expression of surface morphology.

The second important point is that the relationship of gyrification and brain size is group specific."

from welker 1959:

"The second main hypothesis supported by the experiments reported here is that cortical sulci are formed at the boundaries of physiological subdivisions. Each of these physiological subdivisions (e.g., the cortical representations of the separate digits) presumably subtends discrete bundles of afferents (and their terminals) which are differentiated from one another not only spatially but by their synaptic connections to discrete and separate regions at the periphery. Since the evoked potentials are largest there, the crown of a gyrus apparently receives a dense bundle of afferents from a correspondingly richly innervated sensory surface (e.g., the

distal eminence of a digit). The region which forms the fundus of a sulcus, or incipient suleus, on the other hand, presumably receives relatively sparse innervation from the periphery (e.g., digit dorsum or proximal portion of a digit) since the evoked responses there are minimal or nonexistent. Brain sections stained with licmatoxylin indicate that there is a greater density of myeliriated fibers at the gyral crowns than at the fundi in the somatic region of the raccoon. At any rate, these data suggest that the cortex of the gyral crowns is functionally more active than that of the fundi.

To extend the hypothesis, it would seem that during ontogenetic development of the cerebral cortex tlie cortical terminals from densely innervated regions push upward and outward, while sparsely innervated areas are left behind to become the fundi. The dynamics of sulcus formation, then would more likely be conceived of as a mushrooming, rather than as an infolding of cortex. Whether or not sulci in other regions of the cerebral cortex or in the cortex in other animals bear the same relationships to physiological or anatomical subdivisions as they do in SI of the raccoon remains to be demonstrated in detail. Rome evidence (Connolly, '50) indicates

that such a correlation is often found in primate brains. The mechanism which might regulate such selective gi+owth of corticopetal connections may involve biochemical factors as suggested by Sperry (51). That the particular shape of cortical sulci may be influenced by limitations imposed on growth by the skull has been suggested by Clark ( '45).

Individual differences in directional orientation and topographic location of sulci is a common finding among animals of a given species. Factors which produce such variability in tlie growth of individual brains are unknown at present but our data indicate that despite such Variability, the sulci faithfully separate physiologically distinct subdivisions."

from Campbell 2002:

"Radial glial cells create boundaries in the developing brain to limit neuronal migration [46-48]."

Fukunishi 2006 Development of cerebral sulci and gyri in fetuses of cynomolgus monkeys

Kashima 2008 Development of cerebral sulci and gyri in fetuses of cynomolgus monkeys (Macaca fascicularis). II. Gross observation of the medial surface

Heritability

Heritability [r]: Add brief definition or description

Keller_2006_Resolving the paradox of common harmful heritable mental disorders:

"finding positive heritability for a mental disorder does not vindicate the mental disorder as a diagnostic category. To a first approximation, every reliably measured behavioral trait shows positive heritability even constructs such as television viewing

(Plomin et al. 1990) and political attitudes (Eaves et al. 1999). Any arbitrary disorder composed of unrelated but heritable symptoms will show credible heritability. Last, heritability is a statistical construct that averages over a lot of complexity. The causal pathways between genes and the heritable behaviors they influence must be mediated by many factors, both genetic and environmental

in nature. If these factors differ across populations, cohorts, or environmental conditions, then heritability estimates and even the specific genes responsible for the heritability might also differ across populations, cohorts, or environmental conditions."

Human uniqueness

Human uniqueness [r]: Add brief definition or description

Vallender 2008b

"A Footnote on Anthropocentrism

In the course of these studies, it becomes inevitable

that there is talk of anthropocentrism. Several factors

should be made clear: First, there is no scientific reason

to think that the lineage leading to humans is privileged

or otherwise different from the lineages leading to other

species. It might be the case that the mechanisms driving

the emergence of the human phenotype vary somewhat

from other species, but this is probably not true and no

evidence has been presented indicating that this is the

case. Second, that positive selection was at work on the

human brain should not come as a surprise or otherwise

set it apart from other phenotypes. Indeed, we are interested

in the brain because, as humans, it is such a major

part of who we are. Behaviors, psychiatric disorders,

emotions, language, all of these intrigue us and warrant

the study of the brain. Other traits unique to humans,

such as the changes in body hair and sweat glands related

to a novel thermoregulatory strategy, are equally important

and warrant study. Finally, the same studies can, and

likely will, be done for any species. We can legitimately

ask what makes a mouse so mousy or a cat so catty. The

methodologies will be largely similar and we will expect

to see the same sorts of results. That these studies generally

take a back seat in visibility to those in humans does

not reflect on the science itself, but rather on the priorities

of our human society."

Image segmentation

Image segmentation [r]: Add brief definition or description

Khairy 2007:

"marching cubes algorithm (Lorensen and Cline,

1987)."

"The polygonalization of the RBF is performed using a

marching tetrahedra variant that has been optimized for

surface following (Treece et al., 1999)."

Crum_2003_Zen_and_the_art_of_medical_image_registration_correspondence_homology_and_quality.pdf

Internet addiction

Internet addiction [r]: Add brief definition or description

Zhou Y, Lin FC, Du YS, Qin LD, Zhao ZM, Xu JR and Lei H (2009). "Grey matter abnormalities in Internet addiction: A voxel-based morphometry study". Eur J Radiol. DOI:10.1016/j.ejrad.2009.10.025. PMID 19926237. Research Blogging. ^[e]

Large Hadron Collider

Larynx

Larynx [r]: Add brief definition or description

Jeffery 2003 Brain expansion and comparative prenatal ontogeny of the non-hominoid primate cranial base:

"The similarities in the direction of angulation suggests that perhaps the same factor is influencing the cranial base in the macaques, howler monkeys, and modern humans. Of the many possible factors, the most obvious from the hrMR images is the size of the upper airway, particularly the larynx. Sagittal images show that even at the earliest stages of fetal life, the larynx in Alouatta is much larger than that in the fetal macaque, which in turn is larger than that in the human fetus (Fig. 9). These size differences seem to match differences in CBA, indicating that the two could well be correlated (see Schon, 1976; Laitman et al., 1977, 1978, 1979; Laitman and Reidenberg, 1993). Clearly, a study of the potential influence of upper airway growth on the fetal basicranium is warranted."

and

"Thus, it seems plausible that the structural impact of brain enlargement on the basicranium is manifested in the primate embryo,

not in the fetus or the infant, and that the resulting flexion is carried through to adulthood with only minor alterations of angulation en route due to growth of other soft-tissue structures such as the larynx."

Laughter

Laughter [r]: Add brief definition or description
A contagious example

Longevity

Longevity [r]: Add brief definition or description
TED Talk by Dan Buettner: How to live to be 100+

Magnetic monopole

Maze

Maze [r]: Add brief definition or description
Lagzi I, Soh S, Wesson PJ, Browne KP, Grzybowski BA (2010). "Maze Solving by Chemotactic Droplets". J Am Chem Soc. DOI:10.1021/ja9076793. PMID 20063877. Research Blogging. ^[e]

Demonstrates that a droplet of mineral oil containing 2-hexyldecanoic acid can successfully navigate a maze if a pH gradient is established by soaking a small block of high gel strength agarose in HCl and putting it at the end opposite to that in which the droplet is released.

See also the supplementary videos at the journal's site.

Mental disorder

Mental disorder [r]: Add brief definition or description

Wilson in Keller 2006:

"mental disorder, is a fallacious, intrinsically non-

Linnaean pseudotaxon. This construct so broadly conflates

distinct moieties schizophrenia, depression, mania, diverse

phobias, and even mental retardation that it is ultimately

without demonstrable naturalistic validity."

Möbius strip

Möbius strip [r]: Add brief definition or description

Mathematically Correct Breakfast — How to Slice a Bagel into Two Linked Halves

Moon

Moses effect

Moses effect [r]: Add brief definition or description

(Schenck 2005): "If a trough of water with a free surface is placed along the axis of a powerful horizontal cylindrical magnet, it is possible to demonstrate the repulsion of the diamagnetic water by the magnetic field (Ueno and Iwasaka, 1994)."

Ask Ueno for image.

Multicellularity

Multicellularity [r]: Add brief definition or description

Boraas 1998 Phagotrophy by a flagellate selects for colonial prey: A possible origin of multicellularity

Music

Music [r]: Add brief definition or description
Susan Savage-Rumbaugh on her research with apes — a talk given at the TED conference 2004

2:00 states that Tasmanian may have had no music

Music perception

Music perception [r]: Add brief definition or description

fritzsch 2006 ear development morphogenesis.pdf:

"We recently provided new insights into the evolution of

the auditory system, including the cochlea (Fritzsch et al.,

2006)"

Fritzsch, B., Pauley, S., Feng, F., Matei, V., Nichols, D.H., 2006. The

evolution of the vertebrate auditory system: transformations

of vestibular mechanosensory cells for sound processing is

combined with newly generated central processing neurons.

Int. J. Comp. Psychol. 19, 124.

Fujioka 2003 Tonotopic representation of missing fundamental complex sounds in the human auditory cortex

Bermpohl 2006 Attentional Modulation of Emotional Stimulus Processing: An fMRI Study Using Emotional Expectancy

Bieser 1996 Auditory responsive cortex in the squirrel monkey: neural responses to amplitude-modulated sounds

Lefebvre 2008:

"Lesion and neuronal recording techniques are useful in identifying precise areas crucial to the correct functioning of a given cognitive system, but they are incapable of mapping the whole set of areas that are active. In contrast, techniques like MRI, immediate early genes and receptor site mapping can inform us about how broad or localized should be our search for brain correlates of cognition. The techniques routinely compare neural activation during a particular cognitive task [e.g., imitation of observed movement, Iacoboni et al., 1999] to that of the closest control (e.g., movement or observation only), and thus underestimate the total number of brain areas active during cognitive processing. Bearing this in mind, the most frequent result of brain imaging studies is that a number of different localized centers distributed all over the brain are involved in each cognitive activity. For example, a meta-analysis of 64 MRI studies in humans reveals a very broad distribution of areas active in different types of human tool use situations [Lewis, 2006]. When the mapping of the areas is restricted to those that are reported in at least four of the 64 studies, eight areas in the cortex, plus areas in the cerebellum and basal ganglia appear to be involved. During macaque tool use, 10 areas show MRI activity, from different parts of the right and left cerebellum to parts of the basal ganglia and cortical areas such as the precuneus and inferior temporal cortex [Obayashi et al., 2001]. During cooperative interactions in a prisoners dilemma game, at least five cortical and subcortical areas are active in humans [Rilling et al., 2002]."

Neuroimaging

Neuroimaging [r]: Add brief definition or description

"increasing cognitive capacity during childhood may coincide with a gradual loss rather than formation of new synapses and presumably a strengthening of remaining synaptic connections. It is clear that innovative methods like fMRI together with MRI-based morphometry and nonhuman primate studies will transform our current understanding of human brain development and its relation to behavioral development." \citep{Casey:2000p51495}

NeuroImaging-Platform (NIMG-PF) User Manual

Orang utan

Orang utan [r]: Add brief definition or description

Cited by Hossfeld 2005:

Camper, P., 1784. Kurze Nachricht von der Zergliederung verschiedener Orang-Utans. Herrn Pieter

Campers kleine Schriften. Part 2, vol. 1. Verlag S. L. Crusins, Leipzig, pp. 65 94.

Camper, P., 1785. Nachricht vom Sprachwerkzeuge des Orang-Utan. Herrn Pieter Campers sämtliche

kleinere Schriften. Verlag S. L. Crusins, Leipzig.

Wich, Serge A.; Karyl B. Swartz & Madeleine E. Hardus et al. (2009), "A case of spontaneous acquisition of a human sound by an orangutan", Primates: in press, DOI:10.1007/s10329-008-0117-y ^[e]
A video from the supplementary material of
Wich, Serge A.; Karyl B. Swartz & Madeleine E. Hardus et al. (2009), "A case of spontaneous acquisition of a human sound by an orangutan", Primates: in press, DOI:10.1007/s10329-008-0117-y ^[e], showing a whistling 30-year old orangutan:

Pathology

Pathology [r]: Add brief definition or description

http://www.flickr.com/photos/euthman/270606087/

Peer review

"What is important here is not the truth or falsity of the assertion of Chuine et al. about Burgundy temperatures. Rather, what is important is that a paper on what is arguably the world's most important scientific topic (global warming) was published in the world's most prestigious scientific journal with essentially no checking of the work prior to publication."

Permutation

Phenology

"The USA National Phenology Network brings together citizen scientists, government agencies, non-profit groups, educators and students of all ages to monitor the impacts of climate change on plants and animals in the United States. The network harnesses the power of people and the Internet to collect and share information, providing researchers with far more data than they could collect alone."

Plasma

Psychiatry

Psychiatry [r]: Add brief definition or description
The Amazing World of Psychiatry - a blog about psychiatric research

Psychophysics

Psychophysics [r]: Add brief definition or description
A series of optical illusions

Research

Research [r]: Add brief definition or description

Kaplan K (2009). "Unmasking the impostor.". Nature 459 (7245): 468-9. DOI:10.1038/nj7245-468a. PMID 19582885. Research Blogging.

RNA world

In my eyes Nobel-worthy

Sauropod

Sauropod [r]: Add brief definition or description

Open questions

1====Open questions===1

How did sauropods actually swallow?

Scholarly wiki

Scholarly wiki [r]: Add brief definition or description

Wada 2006:

"Figs. 1021, Tables 16, and Appendix, which are published as supporting information on the PNAS web site, all cited below, show additional information."

Sex determination

Sex determination [r]: Add brief definition or description

Schlichting 2008:

"Kim et al. (2006) reported that applying methyl farnesoate, a juvenile hormone for crustaceans, to females produced males in four species of cladocerans. The surprise of this result was not in the production of males per se, because methyl farnesoate treatment was already known to induce males in Daphnia, but the fact that, for three of these species, males had never been seen before. This unusual perturbation of the internal environmental system has produced a plastic response, a male, that is an alternative phenotype of the genome of the female (Minelli & Fusco 2006)."

Kim, K., A.A. Kotov & D.J. Taylor. 2006. Hormonal induction of undescribed males resolves cryptic species of cladocerans. Proc. R. Soc. Lond. B Biol. Sci. 273: 141147.

Minelli, A. & G. Fusco. 2006. Water-flea males from the netherworld. Trends Ecol. Evol. 21: 474476.

Shape description

Shape description [r]: Add brief definition or description

Mak 2007:

"Here, we present a new moment method for describing and comparing molecular shapes in 3D. This method may be viewed as an extension for the spherical harmonics expansion that employs Zernike radial functions [15] to sample objects over regions rather than surfaces."

[15] F. Zernike, Diffraction theory of the cut procedure and its improved form, the phase contrast method, Physica 1 (1934) 689704.

"See Zhang and Lu [16] for a review on shape description"

[16] D. Zhang, G. Lu, Review of shape representation and description techniques, Pattern Recog. 37 (2004) 119.

"An extension of the spherical harmonic expansion method is presented here that enables regions (bodies) rather than contours (surfaces) to be described and which lends itself favourably to the construction of rotationally invariant shape descriptors."

"The extension of spherical harmonics to incorporate radial sampling, whilst taking care to maintain the desirable orthonormality and completeness relationships, has led to the construction of functions equivalent to 3D Zernike functions.We have shown that these functions are well-suited to present molecular shapes and can successfully overcome some of the limitations of surface harmonics. This extra power comes at an additional computational cost per coefficient and also in that many more coefficients are required for the reconstruction. For shape matching, however, rotationally invariant descriptors may be employed thus reducing the number of coefficients greatly."

-->!"Although, the reconstruction quality is superior compared to the pure spherical harmonics approach, the improvement in terms of classification and shape matching is only marginal."

Khairy 2008:

"The prior information about the topology of a 3D object

can be utilized by parameterizing the shape mathematically

(Terzopoulos et al., 1988; Staib and Duncan, 1996)."

Kass, M., Witkin, A., Terzopoulos, D., 1988. Snakes: active contour models. International Journal of Computer Vision 1, 321331.

Staib, L.H., Duncan, J.S., 1996. Model-based deformable surface finding for medical images. IEEE Transactions on Medical Imaging 15 (5), 720731.

Terzopoulos, D., Witkin, A., Kass, M., 1988. Constraints on deformable models: recovering 3D shape and nonrigid motion. Artificial Intelligence 36 (1), 91123.

D. Healy, D. Rockmore, P. Kostelec, and S.Moore. FFTs for the 2-sphere improvements and variations. The Journal of Fourier Analysis and Applications, 9(4):341385, 2003.

Shen 2006:

"Using SPHARM, many tasks can be accomplished in the frequency domain more efficiently, such as shape matching, surface denoising, shape analysis [17]"

[17] S. C. Joshi, M. I.Miller, and U. Grenander. On the geometry and shape of brain sub-manifolds. Int. J. of Pat. Rec. & Art. Int., Special Issue on MRI, 11(8):13171343, 1997.

Morris 2005:

"A novel technique is presented for the comparison of protein binding pockets. The method uses the coefficients of a real spherical harmonics expansion to describe the shape of a proteins binding pocket. Shape similarity is computed as the L2 distance in coefficient space. Such comparisons in several thousands per second can be carried out on a standard linux PC."

Q:How are the L2 distance and L2 norm defined?

"Mathematically there are severalways of describing and representing shapes including triangulations, polygons, distance distributions

and landmark theory. The focus here will be on functional forms. Functions can be either local (piecewise, such as splines) or global in which the whole shape is described by an often very complex expression. Global representations are often termed parametric as the whole shape can be reduced to a number of parameters and each parameter affects the entire shape. Functions can either be explicit, meaning that one coordinate is expressed in terms of the others, or implicit, meaning that the surface points satisfy a given equation (isosurfaces). For example, spherical harmonics can be used for explicit functions, whereas super- and hyperquadrics are implicit representations."

Shimming

Shimming [r]: Add brief definition or description

cite M.J.E. Golay, Field homogenizing coils for nuclear spin resonance instrumentation, Rev. Sci. Instrum. 29 (1958) 313.

Single-nucleotide polymorphism

Single-nucleotide polymorphism [r]: Add brief definition or description

Gibson 2008:

"Single Nucleotide Polymorphisms (SNPs, pronounced snips), which are variations in single bases that occur on the order of one per 100 bases of DNA (Gregory

& Gilbert, 2005)."

Gregory, S., & Gilbert, J. (2005). Strategies for genotype generation. In Haines, J. L., Korf, B. R., Morton, C. C.,

Seidman, C. E., Seidman, J. G., & Smith, D. R. Eds. Current protocols in human genetics (Vol. S47). New

York, NY: Wiley and Sons, Inc.. pp. 1.3.11.3.16.

--> look for other source

Solar eclipse

Solar eclipse [r]: Add brief definition or description

Spherical coordinates

Spherical coordinates [r]: Add brief definition or description

(theta) is taken as the polar (colatitudinal) coordinate

(phi) as the azimuthal (longitudinal) coordinate

Spherical harmonics

Spherical harmonics [r]: Add brief definition or description

Morris 2005:

"Spherical harmonics, Ylm(è, ö), are single-valued, smooth (infinitely differentiable), complex functions of two variables, è and ö, indexed by two integers, l and m. In quantum physics terminology, l is the angular quantum number and m the azimuthal quantum number. Roughly speaking, l gives the number of local minima of the function and therefore represents a spatial frequency. [See any quantum mechanics or functional analysis textbook for more definitions and properties, e.g. Cohen-Tannoudji et al. (1977) and Edmonds (1996).] Spherical harmonics form a complete set of orthonormal functions and thus form a vector space analogue to unit basis vectors. In the same way that vector projections onto each axis (scalar product between vectors) can be used to describe any vector in the familiar form x = (x, y, z)T, expansion coefficients (scalar product between functions) can be used to describe functions. Any (square-integrable) function of Æ and Ó can be expanded as follows: f (Æ, Ó) = �l =0 l �m=.l clmYlm(Æ, Ó). (1)

Note that this expansion is exact and not merely an approximation. Errors are introduced by limiting the series to a certain order of l. A second source of error arises from the fact that the surface to be modelled need not be a function of Æ and Ó. For a closed surface in 3D to be single-valued and therefore a function of Æ and Ó requires that any ray leaving the expansion centre should only penetrate the surface once, i.e. a continuous mapping exists between the surface and the unit sphere S2. Such figures are called single-valued surfaces or star-shape surfaces (Fig. 1)."

"As spherical harmonics enjoy mathematically convenient rotational propertiesthe coefficients can be rotated in the same way as vectors with so-called Wigner matrices (Edmonds, 1996; Chaichian and Hagedorn, 1997)the orientation convention introduced above is merely to speed up the process by avoiding the need to search for optimal rotations between coefficients."

"Another approach would be either to store and search for all axis flips or to fall back on the optimization problem of finding the best alignment. An attractive alternative would be the use of rotationally invariant descriptors (Kazhdan et al., 2003)."

--> Kazhdan,M., Funkhouser,T. and Rusinkiewicz,S. (2003) Rotation invariant spherical harmonic representation of 3D shape descriptors. In Kobbelt, Schröder and Hoppe (eds) Eurographics Symposium on Geometry Processing. EG Digital Library.

Mak 2007:

"Here, we present a new moment method for describing and comparing molecular shapes in 3D. This method may be viewed as an extension for the spherical harmonics expansion that employs Zernike radial functions [15] to sample objects over regions rather than surfaces."

[15] F. Zernike, Diffraction theory of the cut procedure and its improved form, the phase contrast method, Physica 1 (1934) 689704.

"An extension of the spherical harmonic expansion method is presented here that enables regions (bodies) rather than contours (surfaces) to be described and which lends itself favourably to the construction of rotationally invariant shape descriptors."

"The extension of spherical harmonics to incorporate radial sampling, whilst taking care to maintain the desirable orthonormality and completeness relationships, has led to the construction of functions equivalent to 3D Zernike functions.We have shown that these functions are well-suited to present molecular shapes and can successfully overcome some of the limitations of surface harmonics. This extra power comes at an additional computational cost per coefficient and also in that many more coefficients are required for the reconstruction. For shape matching, however, rotationally invariant descriptors may be employed thus reducing the number of coefficients greatly."

-->!"Although, the reconstruction quality is superior compared to the pure spherical harmonics approach, the improvement in terms of classification and shape matching is only marginal."

check Koenderink, J. J. (1990) Solid Shape, MIT Press, Cambridge, MA.

(cited by duncan & olson 1993)

add some of the brain papers

e.g.

G. Gerig, M. Styner, et al. Shape analysis of brain ventricles using SPHARM. In IEEE MMBIA, pages 171178, 2001.

add SPHARM to external links

C. Brechbühler, G. Gerig, and O. Kubler. Parametrization of closed surfaces for 3D shape description. Computer Vision and Image Understanding, 61(2):154170, 1995.

Shen 2006: "Many graphical models do not have genus-zero surfaces. But using a method described in [24], SPHARM can be extended to process arbitrary manifold meshes."

[24] K. Zhou, H. Bao, and J. Shi. 3D surface filtering using spherical harmonics. CAD, 36(4):363375, 2004.

Penna 2007

"The standard method for fitting a sphere-like surface to a data set involves (after a possible translation of coordinate axes) writing

(rho) as a function of the form

(3)".

"We propose to fit a sphere-like surface to a data set by using functions of the form

(5)"

"approximating a data set by (5) can produce results no worse than those obtained using spherical harmonics."

Appendix at http://computer.org/tpami/archives.htm

Shen 2006:

"The spherical harmonic expansion described above is essentially the Fourier transform for functions defined on the sphere; and it transfers spherical scalar signals into its frequency spectrum."

"Since spherical harmonics form a complete set of orthonormal basis functions with a coarse-to-fine hierarchy, using more coefficients leads to a more accurate reconstruction."

Kugelfunktionen:

Lindner (Grundkurs Theoretische Physik, Teubner 1997) writes:

"4.3.9 Kugelfunktionen

Sie sind die Ortsdarstellung der Bahndrehimpulseigenzustände |l,m>. Allerdings kommt es nicht auf den Betrag des Ortsvektors an, sondern nur auf die Richtung (footnote: Einige bevorzugen daher den Namen Kugelflächenfunktionen, der mir aber zu umständlich vorkommt - wir sprechen ja auch von Kugelsymmetrie)."

Subversion

Sulcus

Sulcus [r]: Add brief definition or description

List of sulci, with brief characterization following Ono

Surface tension

Surface tension [r]: Add brief definition or description
Water droplet bouncing off water surface

Syrinx

Syrinx [r]: Add brief definition or description

veney 2005 syrinx.pdf :

"The song system of zebra finches is highly sexually dimorphic (Nottebohm and Arnold 1976). Many features of this circuit, from the forebrain nuclei involved in coordinating motor patterns to the vocal organ in the throat critical for sound production (syrinx), are

enhanced in males compared to females (reviewed in Arnold 1997; Wade 2001; Balthazart and Adkins-Regan 2002). In the forebrain, the volume of song control regions is larger in males than in females, which results from males having larger and more numerous neurons

with more extensive dendritic arborization (reviewed in Arnold 1992). The syrinx, which has been studied much less, is located at the junction of the trachea and the two bronchi and consists of closely spaced cartilage rings enveloped by several bilaterally paired muscles. The largest of these muscles are the ventralis and dorsalis, which together with the others, control the movement of

the syrinx and modulate the flow of air in a manner that in males results in the stereotyped vocalizations typical of song (King 1989; Suthers 1997; Goller and Larsen 2002; Larsen and Goller 2002)."

Transsib

Transsib [r]: Add brief definition or description

Full journey online

Twin

Twin [r]: Add brief definition or description
Souter, V.; M. Parisi & D. Nyholt et al. (2007), "A case of true hermaphroditism reveals an unusual mechanism of twinning", Human Genetics 121 (2): 179–185, DOI:10.1007/s00439-006-0279-x ^[e]

Quotes from abstract: "Traditionally twins are classified as dizygous or fraternal and monozygous or identical ... We report a rare case of 46,XX/46,XY twins: Twin A presented with ambiguous genitalia and Twin B was a phenotypically normal male. These twins demonstrate a third, previously unreported mechanism for twinning. ... Most significantly the twins shared 100% of maternal alleles and approximately 50% of paternal alleles in DNA analysis of skin fibroblasts. The twins are chimeric and share a single genetic contribution from their mother but have two genetic contributions from their father thus supporting the existence of a third, previously unreported type of twinning."

Twitter

Ubuntu

Vocal learning

Vocal learning [r]: Add brief definition or description

"Names" in spectacled parrotlets, Forpus conspicillatus (Wanker 2005) and in Tursiops (Janik papers)

on candidate genes:

candidate processes

-see also Fig. 6A & C in Spiteri 2007 & Tab. 3 in Vernes 2007

Teramitsu 2008 cites

Webb 2005: "FoxP2 in song-learning birds and vocal-learning mammals" at http://jhered.oxfordjournals.org/cgi/content/abstract/96/3/212 .

and

Li, G., Wang, J., Rossiter, S.J., Jones, G., and Zhang, S. (2007). Accelerated FoxP2 evolution in echolocating bats. PLoS ONE 2, e900.

Hall 2007 cites

Remaine, A., 1962. Gedanken zum Problem: Homologie und Analogie, Preadaptation und Parallelitat. Zool. Anz. 166, 447e465.

Pereira 2006 gives molecular divergence as 305-342mybp

see also Benton 2000 (as cited by Blair 2005)

read campbell 2002

Ramus 2006: "The necessary genetic pre-wiring of linguistic modules with

highly speciWc computational properties and connectivity could be obtained through

the joint eVects of (1) genes generally implicated in brain development processes (like

the neural migration genes just discussed) (2) genes with speciWc anatomical expressions

that would interact with the former, and (3) transcription factors that would

orchestrate the expression of the former two, so that they would be expressed at speciWc

times, in speciWc combinations and in speciWc areas so as to produce unique anatomical

structures with unique computational and representational properties.

Although the third category of genes might include language-speciWc genes (triggering

developmental cascades relevant only to linguistic modules), they might also have

other regulating functions elsewhere in the brain or in the rest of the body. As seems

to be the case with the FOXP2 gene (see Fisher), such functions could be shared with

other species, with only one or two recent mutations possibly allowing the protein to

perform an additional regulatory function without compromising earlier ones. Such

may be the reality about the genetics of language."

paper by Balaban in Cognition 101, 2006 (cited by ramus):

Evan Balaban goes on with a birds eye view of the multiple factors that influence

brain development, which explain why causal relationships from gene to cognition are

highly degraded. His paper covers further discussion of what FOXP2 may or may not

do, biological determinants of critical periods, experience and brain plasticity, and the

important but often overlooked role of stochastic factors in brain development. He

advocates greater integration between biological data and cognitivist theorising.

To T: Read Ramus 2006, at least section 5:Developmental dyslexia and the future of language genetics

Ramus 2006:

"Until recently, linkage studies had provided six reliable chromosomal loci suspected

to harbour genes associated with dyslexia (Grigorenko, 2003). Now four such

genes have been identiWed in some of these loci: DYX1C1 on 15q21 (Taipale et al.,

2003), KIAA0319 on 6p22 (Cope et al., 2005; Francks et al., 2004), DCDC2 just a few

markers away on 6p22 (Meng et al., 2005; Schumacher et al., 2005), and ROBO1 on

3p12 (Hannula-Jouppi et al., 2005). If it were not exciting enough to discover four

dyslexia genes in two years, functional studies of these genes have provided remarkably

converging evidence.

LoTurco and colleagues have used a particularly innovative technique to study

the role of three of these genes in brain development (Bai et al., 2003). They have produced

functional knock-out rats using in vivo RNA interference. This technique

allowed them to speciWcally block the translation of the gene of interest, in vivo,

locally, and at a chosen stage of development (indeed, in utero during neural migration).

Using this technique, they showed that DYX1C1 is involved in radial neural

migration, and that the part of the protein that is truncated in a Finnish dyslexic family

(Taipale et al., 2003) is necessary and suYcient for normal neural migration

(Wang et al., submitted for publication). They have further shown that cortical ectopias

(like the ones observed in dyslexic brains) sometimes occur as a result of the

DYX1C1-induced disruption of neural migration. The same team has been able to

conduct similar studies on both DCDC2 (Meng et al., 2005) and KIAA0319 (Paracchini

et al., 2006), again concluding that these genes are crucially implicated in neural

migration. Finally, ROBO1 is a homologue of a well-known drosophila gene that is

involved in inter-hemispheric axon guidance and cortical dendritic guidance (Hannula-

Jouppi et al., 2005).

Amusingly, these Wndings oVer a striking parallel with Galaburdas original discovery

of the Wrst four brains with neural migration anomalies. Now there are four

candidate genes for dyslexia, and all four are involved in neural migration or guidance.

How likely is that to occur by chance?

-->Perhaps the hypothesis that dyslexia is a

neural migration disorder should be taken seriously at last.

"This suggests that other genes remain to be found, whose expression

in the cortex is anatomically restricted, and that interact with neural migration

genes in such a way as to spatially constrain the eVects of risk alleles. As I have mentioned

earlier, there are plenty such genes, the latest search yielding 349 (Gray et al.,

2004)."

add Kuypers, 1958/ Jürgens, 1998.

User:Daniel Mietchen/Notes to self: Difference between revisions

Latest revision as of 09:27, 1 April 2024

Notes to self

Bookmarks

Within CZ

Special pages

Templates

Images

Bot support

Implemented

Just a thought

Categories

Charter

Within WP

MediaWiki extensions

Other

Workgroups

Interesting research papers

Flow

Videos to watch

Watched

Featured images

Get current source

Orphaned subpages

Offline notes

Abstract (publishing)

Animal

Arctic

Arnold Dohmen

Astrolabe

Aurora borealis

Bagel

Bionics

Billion

Biomechanics

Blind spot

Brain development

Brain evolution

Brain function

Brain morphometry

Brain plasticity

Brain size

Chaos

Charles Bonnett syndrome

Cleavage plane orientation

Cluster analysis

Colour blindness

Comparative biology

Cordyceps

Cryobiology

Cryptobiosis

Deep homology

Minelli

Dionaea muscipula

Dodo

Embryo

Emotion

Encephalization

Epigenetics

Erwin Neher

Evolution

Expertise

Fetus

Paul Feyerabend|Feyerabend, Paul

Fractal dimension

Gyrification

Heritability

Human uniqueness

Image segmentation

Internet addiction

Large Hadron Collider

Larynx

Laughter

Longevity

Magnetic monopole

Maze

Mental disorder

Möbius strip

Moon

Moses effect