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

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*[http://www.mediawiki.org/wiki/Help:Extension:ParserFunctions ParserFunctions]
*[http://www.mediawiki.org/wiki/Help:Extension:ParserFunctions ParserFunctions]
*[http://www.semantic-mediawiki.org/wiki/Semantic_MediaWiki Semantic MediaWiki]
*[http://www.semantic-mediawiki.org/wiki/Semantic_MediaWiki Semantic MediaWiki]
*[http://www.bioinf.mvm.ed.ac.uk/twiki/bin/view/TWiki/BioKbPlugin biological knowledgebase]
:[http://www.biomedcentral.com/1471-2105/10/291 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.
*[http://www.mediawiki.org/wiki/Extension:Simple_namespaces Simple namespaces]
*[http://www.mediawiki.org/wiki/Extension:Simple_namespaces Simple namespaces]
*[http://www.mediawiki.org/wiki/Extension:Widgets Widgets] (incl. Slideshare)
*[http://www.mediawiki.org/wiki/Extension:Widgets Widgets] (incl. Slideshare)

Revision as of 15:48, 18 September 2009

Notes to self

Bookmarks

more here

Within CZ

Special pages

"Newbie" contribs

Templates

Images

Bot support

Implemented

See also the list of scripts I ran.

Just a thought

May be useful to

Categories

Within WP

sample edit
Citation bot
see also http://en.wikipedia.org/wiki/User:Benc/Scripts/what_links_out.py

MediaWiki extensions

Full 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.

Other

{{#ev:vimeo|5772930}}

see also Rejecta Mathematica
{{#ev:youtube|HqT_fokXsss}}
{{#ev:youtube|CxK20wvjDLM}}

"It is impossible to devise an experiment without a preconceived idea; devising an experiment, we said, is putting a question ; we never conceive a question without an idea which invites an answer. I consider it, therefore, an absolute principle that experiments must always be devised in view of a preconceived idea, no matter if the idea be not very clear nor very well defined."

{{#ev:youtube|SPtMMPE1IDQ}}
{{#ev:youtube|xhzXWX-WASg}}
{{#ev:youtube|XZKyXpqHmDc}}
{{#ev:youtube|CU2vl0RlMxw}}
{{#ev:youtube|zPfrGrpkA8M}}
{{#ev:youtube|vrh99kKfUkw}}
See also the CZ tag at YouTube
  • A short video documentary about the Science Busters, an Austrian science comedy (in German):
{{#ev:youtube|aNitjcZ0D1k}}
{{#ev:youtube|6Sm2-klwTUs}}

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 banner.png
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:

Subpage categories:

Missing subpage categories:

Article statuses:

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:

Subpage categories:

Missing subpage categories:

Article statuses:

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:

Subpage categories:

Missing subpage categories:

Article statuses:

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 16,468 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
add co-authors
add co-authors
  • 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.
  • 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.
  • 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


Videos to watch

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

{{#ev:vimeo|5676816}}

puts the Origin of species at 1879 but otherwise, it's fascinating.
brief overview of history of gene sequencing
Announcement of a new internet protocol that may turn out to be very interesting in a scientific context
a shout-out for "Raw Data Now", nice intro for those who never heard of Open Data initiatives before
about the power of being nice; too long for my taste (I stopped after 5:34 min)

Get current source

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

Orphaned subpages

{{#ev:youtube|bVhOntMCmnQ}}

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.


Animal

Arctic

Arnold Dohmen

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.

see also CZ:Ref:Dohmen 1941 Anleitung zu physikalischen Untersuchungen an Hirn und Schädel bei der Leiche
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.

Aurora borealis

Bionics

Billion

Quotes:

Biomechanics

Gordon_2006_Mechanics_in_embryogenesis_and_embryonics_prime_mover_or_epiphenomenon.pdf

Blind spot

Brain development

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), S35–S45.


Agarwala, S., Sanders, T.A. and Ragsdale, C.W. (2001) Sonic hedgehog control of size and shape in midbrain pattern formation. Science, 291, 2147–2150.


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

Brain evolution

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 72:106–122.

--> get it!

Levitt, P. (2003) Structural and functional maturation of the developing primate brain. J. Pediatr., 143 (Suppl. 4), S35–S45.

Brain function


Brain morphometry

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 Goodson’s 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: 223–236.

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

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), 300–307.

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: Otx2’s 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

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, 125–140.




Chaos

Cleavage plane orientation

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 Valles et al. (2002). 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
see also Huttner 1997

Comparative method

Sherry. NEUROECOLOGY. Annu. Rev. Psychol. 2006. 57:167–97

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 Goodson’s 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: 223–236.


Cordyceps

{{#ev:youtube|CCOQ0VU24xw}}

Cryptobiosis

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

Deep homology

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: 107–116.

cited by Carroll 2005


More from Carroll 2005:

"Thus, while the coding sequences of the structural and regulatory proteins are constrained by pleiotropy, modular cis-regulatory regions enable a great diversity of patterns to arise from alterations in regulatory circuits through the evolution of novel combinations of sites for regulatory proteins in cisregulatory elements [35]."

35. Gompel N, Prud’homme B, Wittkopp PJ, Kassner VA, Carroll SB (2005) Chance caught on the wing: Cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433: 481–487.

and

"A standard

comparative analysis of the FOXP2

coding sequences of humans and songlearning

and non-learning birds did

not reveal any amino acid substitutions

that were shared between song-learning

birds and humans, nor any fixed

differences between song-learning

and non-learning birds. The study

concluded there was “no evidence for

its [FOXP2] role during the evolution

of vocal learning in nonhuman

animals” [67].

In great contrast, when FOXP2

mRNA and protein expression in

the developing and adult brains of

a variety of song-learners and nonlearners

were examined, a striking

increase in FOXP2 expression was

observed in Area X, a center necessary

for vocal learning that is absent from

non-learners [68] (Figure 3A–3C).

This increase occurs in zebra finches

over the developmental period when

vocal learning occurs. Furthermore,

in adult canaries, seasonal changes

in FOXP2 expression were observed

in Area X, associated with changes in

the stability of the bird’s song (Figure

3D–3F). Thus, remarkable changes in

the regulation of FOXP2, but not the

protein sequence, are correlated with

the development and evolution of

vocal learning in birds. These changes

could arise through the evolution of

FOXP2 cis-regulatory sequences, or of

the regulatory or coding sequences

of transcription factors that control

FOXP2."

67. Webb DM, Zhang J (2005) FoxP2 in songlearning birds and vocal-learning mammals. J Hered 96: 1–5.

68. Haesler S, Wada K, Nshdejan A, Morrisey EE, Lints T, et al. (2004) FoxP2 expression in avian vocal learners and non-learners. J Neurosci 24: 3164–3175.


MANATEE gene annotation software forge.net/


Rehkämper 1991

"Besides diversification, which obviously occurs, parallel evolution may be one of the general features of evolutionary development."

("The difference between parallelism and convergence is whether the two groups, which developed this similarity independently, originate from a common ancestor (parallelism) or not (convergence). However, both have responded to the same selective pressure or have followed the same adaptive trends. This we would like to call "parallel evolution ". It should be stressed that "parallel evolution" does not implicate a decision between convergence and parallelism.")


"brain structure in birds has been studied to test

the hypothesis that, if a considerable adaptive ability

is given, this should be correlated with an expansion

of multimodal integrative areas in the brain."

- also provides data on connectivity patterns in avian and mammalian brains:

"A comparison of the connectivity of the various areas

of the mammalian neocortex with that of the avian ventral

hyperstriatum/neostriatum complex reveals further

similarities, which can now be interpreted as a functional

similarity. The brain regions comprise primary target

areas of the three major sensory systems (visual, auditory

and somatosensory) in the mammalian as well as in the

avian telencephalon. A primary output area can be defined

in both classes. In both classes the primary areas

are surrounded by secondary areas, which are interconnected

with the respective primary areas, e.g. the primary

visual cortex in mammals is connected with a neighbouring

secondary area (Zilles 1985; Zilles and Wree 1985).

This corresponds to the ectostriatum in the pigeon with

a core and a belt region (Karten and Hodos 1970;

Ritchie 1979). The mammalian auditory cortex exhibits

a core (primary) and a belt (secondary) region (Patterson

977), which correspond to the primary area Ne 12 with

the secondary areas Ne 13 and 14 (Rehk/imper et al.

1985). Finally, the mammalian somatosensory cortex

follows the same scheme (Pandya and Yterian 1985).

The equivalent areas in birds are the primary area Ne 1

and the secondary area Ne 2 (Rehk/imper et al. 1985).

The most important aspect, however, is that not only

in the mammalian neocortex, but also in the avian neostriatum

and ventral hyperstriatum, a considerably large

region is occupied by tertiary areas."


Furthermore: "Deduced from a Darwinian theory of evolution with

the central argument of adaptation, it has been hypothesized

that parallel evolution in mammals and birds

should also be found in the brain of both classes. Mammalian

brain evolution is characterized by progressive

encephalization, e.g. in primates, which are a biologically

advantageous group. This progressive encephalization

is mainly a progressive telencephalization, especially

neocorticalization. Principally, the same is found in

birds. Architecture and connectivity of the quantitatively

most progressive brain parts support the hypothesis that

this progression is primarily an enlargement of

multimodal integrational capacities, both in mammals

and in birds. That points to a strongly adaptive character

of neocorticalization and a biological advantage of increased

integrational capacities. It can be concluded that

there is strong selective pressure, which acts in a similar

way in mammals and in birds and leads to parallel brain

evolution."

- nice historical overview, too

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

Emotion

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

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

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

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.,

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

or

  1. 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

Feyerabend, Paul

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

Fractal dimension

Gyrification

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 brain’s 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

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

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

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


Larynx

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."


Magnetic monopole

Mental disorder

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."

Moon

Moses effect

(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

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

Music

  • 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

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, 1–24.


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 prisoner’s dilemma game, at least five cortical and subcortical areas are active in humans [Rilling et al., 2002]."


Neuroimaging

"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

  • 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.

{{#ev:youtube|CxK20wvjDLM}}

Pathology

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."

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."
See also this blog post about it.

Psychiatry

The Amazing World of Psychiatry - a blog about psychiatric research


RNA world

In my eyes Nobel-worthy

Sauropod

Open questions

Scholarly wiki

Wada 2006:

"Figs. 10–21, Tables 1–6, and Appendix, which are published as supporting information on the PNAS web site, all cited below, show additional information."

Sex determination

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: 141–147.
  • Minelli, A. & G. Fusco. 2006. Water-flea males from the netherworld. Trends Ecol. Evol. 21: 474–476.


Shape 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) 689–704.


"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) 1–19.


"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, 321–331.


Staib, L.H., Duncan, J.S., 1996. Model-based deformable surface finding for medical images. IEEE Transactions on Medical Imaging 15 (5), 720–731.


Terzopoulos, D., Witkin, A., Kass, M., 1988. Constraints on deformable models: recovering 3D shape and nonrigid motion. Artificial Intelligence 36 (1), 91–123.


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):341–385, 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):1317–1343, 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 protein’s 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

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

Single-nucleotide polymorphism

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. 1.3.1–1.3.16.

--> look for other source

Solar eclipse

{{#ev:youtube|MuNVnsg7XeI}}

Spherical coordinates

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

(phi) as the azimuthal (longitudinal) coordinate

Spherical harmonics

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 ƒÆ and ƒÓ can be expanded as follows: f (ƒÆ, ƒÓ) = ‡�l =0 l �m=.l clmYlm(ƒÆ, ƒÓ). (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 ƒÆ and ƒÓ. For a closed surface in 3D to be single-valued and therefore a function of ƒÆ and ƒÓ 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 properties—the 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) 689–704.

"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 171–178, 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):154–170, 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):363–375, 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

Syrinx

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)."

Twin

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

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


on candidate genes:


  1. 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 bird’s 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 Galaburda’s 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.

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