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Revision as of 00:43, 10 February 2009

Hourglass drawing.svg Where Daniel lives it is approximately: 10:20

Notes to self

Bookmarks

more here

Within CZ

Special pages

Templates

Images

Within WP

Other

{{#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.

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Interesting research papers

  • 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


Get current source

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

Orphaned subpages

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.


Biomechanics

Gordon_2006_Mechanics_in_embryogenesis_and_embryonics_prime_mover_or_epiphenomenon.pdf


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 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.



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.


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

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, Hacker, Guthrie 2001: mechanisms and molecules in motor neuron specification and axon pathfinding.
  • 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'."

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


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."


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."


Multicellularity

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


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]."


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.


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."


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


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)."


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)."



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.

Talk space

Archives

none (to start Archive 1)


Biology articles started during Biology Week

Daniel, what does this mean:

Please use the format {{rpl|Your Article's name}}.

Will you give an example. --Anthony.Sebastian 22:26, 17 September 2008 (CDT)

Sorry...

It's not Monday anywhere yet, is it? --Larry Sanger 09:15, 21 September 2008 (CDT)

Thanks for checking but according to The World Time Clock, it was Monday on the Christmas Islands (24h ahead of Hawaii) before I put up the notice. Daniel Mietchen 16:51, 21 September 2008 (CDT)

Re your welcome message to newcomer Sjoerd Hoogwater

Hi, Daniel, I don't think we've met before. I noticed in your welcome message on the Talk page of newcomer Sjoerd Hoogwater, at User talk:Sjoerd Hoogwater, that your list of articles indicated that we need articles entitled Refinery and Gas processing. I just want to point out that we already have two very detailed articles entitled Natural gas processing and Petroleum refining processes which cover the subjects of refinery and gas processing quite well. In fact the Petroleum refining processes article is an Approved article.

If you want to see all of the articles currently in the Chemical Engineering field, please visit Category:Chemical Engineering Subgroup which now has 98 articles in it.

Best regards, Milton Beychok 01:29, 24 September 2008 (CDT)

Brain and Music

That's a very impressive brain & music program you've put together. I'll be most interested in the final results. It could be a real contribution to public discourse on the subject. Best of luck. William L. Benzon 14:12, 26 September 2008 (CDT)

Bio Week stats

Sorry for the delay, recently I'm not a frequent visitor here. Stats for the Bio Week may be a good idea. For technical reasons a dump takes a couple of days and it's not possible to do it at a given moment. Not really we need this, since any edit or action is timestamped anyway. It is enough to filter the dump that is usually taken at the beginning of the month. What kind of information would be most interesting in this case? Maybe human-related stats (number of editors, number of edits etc;). Any other ideas? Best, Aleksander Stos 10:00, 27 September 2008 (CDT)

Thanks for combat loading adjustments

I hadn't realized how much obsolete material was still in that article; I've updated it somewhat but it needs much more work. There is relevant material, among other places, at amphibious warfare and prepositioning ship.

One of these days, we really need to link articles where this was an issue. Falklands War is a stub, and there were very unusual cross-loading considerations due to the extreme distance and ad hoc organization, but the loss (especially) of the Atlantic Conveyor, with all but one of the medium/heavy helicopters, is useful as an example. The Bay of Pigs is a stunningly bad example (at the Falklands, they took a calculated risk).

Guadalcanal actually did have some combat loading, but RADM Fletcher didn't give sufficient unloading time. Gallipoli, an interest of mine, also deserves an article as one of the all-time examples of bad senior command, admittedly no amphibious doctrine, and missed opportunities (e.g., Anzac Cove). Howard C. Berkowitz 12:39, 29 September 2008 (CDT)

surprises

What were they in the last set of moves? I plan to fix some of the previous ones you mentioned but you implied there were some new surprises? Chris Day 08:06, 2 October 2008 (CDT)

By the way, thanks for being the guinea pig :) Chris Day 08:06, 2 October 2008 (CDT)

Subsubpages

Many of the lists can live at subsubpages to a catalog subpage. We have a number of stand alone catalogs and lists that need to migrate to more appropriate homes. See:

Chris Day 09:28, 6 October 2008 (CDT)

Article of the week: Hydrogen bond

I just changed the article status of Hydrogen bond from a "3" to a "1". It was nominated for article of the week (front page feature) with yourself as specialist supporter, so I presume from that (as well as from reading it) that it should be a "1".

If it is still the leading vote-getter next Tuesday or Wednesday, I will put it on the front page.

James F. Perry 22:05, 12 October 2008 (UTC)

Should that article be checked "partial content from Wikipedia"? James F. Perry 15:08, 13 October 2008 (UTC)
Yes, and I think it had that but I couldn't find it right now. Please ask someone else to check, as I'm going offline. -- Daniel Mietchen 16:59, 13 October 2008 (UTC)

Piquet

I see you marked this article as incomplete. the template doesn't ask for details, but I wonder whether you have any specific suggestions for the sorts of things you think should be added. Peter Jackson 17:20, 23 October 2008 (UTC)

Peter and Daniel: Excuse me for poking my nose into here. Peter, the status in the Metadata template was marked as a 2 by Daniel. That is a pretty good status rating. To move it up to 1, I would suggest that: (1) The Definition subpage be created and a definition be provided, (2) The Related Articles subpage be created and filled in as best as you can, (3) The Bibliography subpage be created and some books be listed (if possible), and (4) the External Links subpage be created and some links to external websites be provided (if possible). When creating those subpages, be sure that the template {{subpages}} is at the top of each of them.
I don't know enough about the Piquet game to comment on the content, but I would also suggest a very thorough spell check. Hope this helps and best regards, Milton Beychok 17:38, 23 October 2008 (UTC)
I am also not familiar enough with the game to comment on content but I agree with Milton's suggestions and would add that intrawiki links as well as some illustrations would be nice (and useful) additions (e.g. a picture of one the specific situations mentioned in the text). --Daniel Mietchen 18:15, 23 October 2008 (UTC)

Can you help with Meteorology?

Daniel, I've been looking at your user page and the topics in which you are interested. Very impressive, indeed!! A few days ago, I created the Meteorology article because there were dozens and dozens of intrawiki links to that word in a good many CZ articles.

As I wrote on the Talk page of Meteorology, I really have a minimal knowledge of that field. Do you think that you might be able to expand that article ... or do you know someone who can do so?

Thanks for any help you can provide. Milton Beychok 22:19, 23 October 2008 (UTC)

DOI for Lorenz's paper does not work

Daniel, the DOI that you included in the reference for Lorenz's paper in the Meteorology article does not work. Can you correct it? If not, then please just delete that part of the reference. Thanks. Milton Beychok 17:02, 24 October 2008 (UTC)

The DOI is correct but contains < and > signs that cause problems with the citation template. --Daniel Mietchen 14:37, 25 October 2008 (UTC)

Rathaus Leipzig

Hi Daniel, ich bin heute dazu gekommen das Rathaus zu fotografieren. Leider habe ich das Neue Rathaus fotografiert und eben erst bemerkt, dass du das alte haben möchtest :-( ... naja. Ich versuche es die nächsten Tage dann nochmal mit dem alten Rathaus :-) Wie du siehst gibt das Wetter leider momentan keine sehr schönen Bilder her. -- Alexander Wiebel 09:54, 3 November 2008 (UTC)

So ich habe jetzt das richtige Rathaus (mit Weihnachtsmarkt). [1] (die letzten zwei Bilder). Kann sein, dass das mit Markt nicht so gut ist, dann versuch ich es demnächst nochmal. Kommentare? -- Alexander Wiebel 15:47, 7 January 2009 (UTC)
Ein Bild parallel zur Fassade wär schöner, aber für's Prinzip reicht das. Mit Weihnachtsmarkt ist netter als ohne. Danke erstmal! --Daniel Mietchen 15:51, 7 January 2009 (UTC)
Ich habe versucht es hochzuladen. Wohl so etwa zwazig mal von verschiedenen Rechnern aus verschiedenen Netzwerken mit verschiedenen Browser. Seltsamerweise war es mir nicht möglich das Foto auf den Server zu bringen. Entweder der Broser fror ein, oder ich bekam sowas wie "Connection Interrupted". Strange. -- Alexander Wiebel 22:30, 8 January 2009 (UTC)
Hi Daniel. Mein Problem war, dass die Datei knapp über 2MB war und ich das nicht bemerkt habe. Die Fehlermeldung ist auch alles andere als intuitiv. Altes Rathaus Leipzig.jpg. -- Alexander Wiebel 14:12, 18 January 2009 (UTC)

Your testimony

Bitte let us have it! --Larry Sanger 21:02, 3 November 2008 (UTC)

Done. --Daniel Mietchen 13:51, 2 January 2009 (UTC)

Ethnologue

Hi. Thank you for editing Volga Tatar language, but I think we should avoid links to Ethnologue which do not provide reliable information. A lot of linguists criticize Ethnologue.--Domergue Sumien 15:14, 6 November 2008 (UTC)

Cette source semble sérieuse et émane de l'Université du Michigan: [2]. Cordialement.--Domergue Sumien 16:39, 6 November 2008 (UTC)

Griechische Buchstaben

Daniel, thank you for the corrections of the formatting of the Greek-letter disambiguation pages by the addition of the (disambig) and (dabhdr) templates. I was not aware of the correct way to annotate them. I will go through the whole alphabet and correct the other pages I have created. Thanks again. Bruce M.Tindall 21:01, 22 November 2008 (UTC)

Plos One

Excellent :) Chris Day 15:09, 5 December 2008 (UTC)

I am always glad when I receive hints that somebody might actually read this stuff. --Daniel Mietchen 19:04, 5 December 2008 (UTC)

Writing an Article - Incrementally

Hello Daniel! Thank you for your warm greetings and kind suggestions. I would like to start an article on protein folding (my passion), but I will not have time to write the entire piece in one sitting. Rather than posting an incomplete article in the public forum, is there a "sandbox" type of application that I can use? Just curious. Otherwise, I will go ahead and begin the page in the usual way. Thanks! Mitchell McGill 18:49, 29 December 2008 (UTC)

Please excuse me for "butting in". I just created that personal sandbox for you, Mitchell. See your user Talk page for discussion on using the sandbox. Enjoy! Milton Beychok 20:31, 29 December 2008 (UTC)

Citation template you recently used

Daniel: You recently added an article citation in Life/Bibliography, using a template I hadn't seen before. I tried it, it didn't work for me, you deleted it.

Will you explain what I did wrong, please. --Anthony.Sebastian 20:55, 31 December 2008 (UTC)

The "template" is transclusion. The problem was that the page you referenced (CZ:Ref:DOI:10.1016/j.shpsc.2006.09.009) did not exist. I just created it via http://toolserver.org/~verisimilus/Scholar/ (the automated reference wikificator suggested at the top of bibliography pages), and put it into the article, along with the abstract. Take another look, preferably in preview and/or diff mode. This kind of reference formatting is part of an experiment I have started in order to make the bibliographies more useful and less tedious to maintain. Your comments on that could be very helpful. I also recently blogged, from a broader perspective, about the topic. --Daniel Mietchen 11:54, 2 January 2009 (UTC)
Daniel, you may have posted this elsewhere and I've missed it, but I assume the series of entries you are creating, which begin CZ:Ref:DOI:..., are some type of common space for bibliographic references. Where can I find more details? I'm very interested in the idea, although I don't think that all of my references will have DOIs. Howard C. Berkowitz 15:09, 18 January 2009 (UTC)
Hi Howard, more details can be found via the above-mentioned experiment. It works similarly well for CZ:Ref:ISBN or other identifiers that map at least injectively (but preferably bijectively) to a bibliographic item. The identifier-based pages do not necessarily bear human-readable names (e.g. CZ:Ref:DOI:10.1371/journal.pone.0001683), and so I have come to make regular use of human-readably shortcuts composed as CZ:Ref:FirstAuthorsLastName_Year_Title_of_the_item_as_it_appears_on_the_cover_page (i.e. CZ:Ref:Stringer 2008 Effectiveness of Journal Ranking Schemes as a Tool for Locating Information). Such a system may also be helpful in cases where no unique identifier is available, as with CZ:Ref:Mountcastle 1957 Modality and Topographic Properties of Single Neurons of Cat's Somatic Sensory Cortex. Pages that I use as a testing ground for this way of reference formatting include the bibliography subpages of gyrification, brain development and pages labeled as using what I call direct referencing. Your comments on usability and pitfalls would be very appreciated. --Daniel Mietchen 10:41, 19 January 2009 (UTC)

Ideal gas law nominated for approval

Hi, Daniel and Happy New year! I have just nominated Ideal gas law for approval. Since I worked on that article to some extent, 2 more Chemistry or Physics editors are required to join in the nomination. I am inviting you join me in the nomination. If you have any questions on how to do that, let me know. Regards, Milton Beychok 20:12, 3 January 2009 (UTC)

I had a quick look and don't think it is ready yet. In brief:
  1. I share Paul's concerns with respect to the (in)elasticity
  2. The sections "Background" and "Special cases" largely overlap, while the article as a whole appears incomplete to me without some derivation from first principles (which could go into an Advanced subpage) and without some specific hints to non-specialists on why this law is important
  3. The Bibliography should contain some of the classic papers
  4. There should be some useful websites (e.g. with applets) to add to the External links

Hope this helps. --Daniel Mietchen 01:25, 4 January 2009 (UTC)

Daniel, would you be so kind as to put your above comments on the Ideal gas law Talk page so that Paul or others will see them and perhaps respond to them? I don't think it would proper for me to move your comments there. Thanks, Milton Beychok 03:30, 4 January 2009 (UTC)
Daniel, please read the "Towards approval" section of the Ideal gas law Talk page where both Paul Wormer and I have made some comments. Also please make whatever changes in the article itself that you think are appropriate. I am hoping that all of us can collaborate in the next few days to bring the article up to the point that it can be approved. I have already made some of the changes suggested by Paul. Regards, Milton Beychok 17:17, 4 January 2009 (UTC)
Daniel, Paul Wormer has now done an extensive re-write of the Ideal gas law article and I would really like to have your collaboration as well. Would you please review, edit and/or comment on the re-written article? Thanks, Milton Beychok 16:44, 5 January 2009 (UTC)
I plan to do that on Wednesday. --Daniel Mietchen 17:51, 5 January 2009 (UTC)
Just a gentle reminder (I hope) that Ideal gas law still seeks your further input. Regards, Milton Beychok 19:15, 10 January 2009 (UTC)
Perhaps no electronic reminder can be gentle enough to handle some sorts of things that happen in meatspace. --Daniel Mietchen 03:08, 11 January 2009 (UTC)
You lost me with "meatspace", did you mean "metaspace"? (:>) In any event, I agree that switching those sections in the Ideal gas law does indeed help with digesting the derivation. Milton Beychok 04:47, 11 January 2009 (UTC)
Still working on the IGL article... For a definition of meatspace, see here. More explanation would require removing this redlink, for which I am not ready yet. --Daniel Mietchen 05:08, 11 January 2009 (UTC)

Culture

Daniel I am hoping your industry will be matched by suitable additions from our colleagues in the Humanities (they must be out there). Aladin 13:34, 7 January 2009 (UTC)

I of course am referring to your inclusions on the disambiguation pages. Aladin 13:37, 7 January 2009 (UTC)

We'll see. --Daniel Mietchen 13:38, 7 January 2009 (UTC)

We are hopeful. Aladin 13:55, 7 January 2009 (UTC)

Appreciation

....just to say how much your great work is appreciatedGareth Leng 15:00, 16 January 2009 (UTC)

Seconded. Daniel, sorry no response to your blog piece. It is in my in-tray. OK, I admit it, under a pile on my desk. I will get to it. Chris Day 15:02, 16 January 2009 (UTC)
Social bookmarking is an old hat by now but I think its potential for scholarly communication has been widely underestimated (or ignored), and this wiki seems to me the currently most suitable platform to promote it. Detailed feedback on the topic (e.g. via this overview table) as well as on the annotation mechanics would certainly find appreciation, too. --Daniel Mietchen 16:11, 16 January 2009 (UTC)

Thanks for your work on Ideal gas law

Daniel, thanks for your work. As I just noted on the Talk page of Ideal gas law, I have now asked Paul to add his signature as the third approval nominator. Milton Beychok 18:39, 16 January 2009 (UTC)

request for approval by an editor

I request you to review the NMR spectroscopy article for approval.Sekhar Talluri 05:15, 17 January 2009 (UTC)

Partition function

Daniel, see here for a proof of Q ≈ qN / N! When you look at it you will understand why I did not include it in ideal gas law. --Paul Wormer 17:04, 22 January 2009 (UTC)

I see. Thanks! --Daniel Mietchen 18:54, 22 January 2009 (UTC)

Thanks

Will do.Gareth Leng 17:06, 22 January 2009 (UTC)

Re: your note on my talk page

I do not think that it is necessary for me to become an editor as far as approval of the NMR spectroscopy article is concerned, as it is clear that there are three well qualified editors - D.E.Volk, Paul Wormer and yourself. Also, we are in the middle of our semester now; our vacation starts in May and hopefully this article will be approved by then - at that time (in May) I can apply to be an editor. 

 Thanks for the invitation.  Sekhar Talluri 17:19, 22 January 2009 (UTC)

Please note my post at Talk:AN- about final approval tomorrow

Daniel, just notifying you about my post at Talk:AN- regarding final approval tomorrow of AN-. Regards, Milton Beychok 05:52, 28 January 2009 (UTC)

Any plans for these?

I can't tell if these are lost or whether they are going to be part of articles? No big deal but just not sure what to do with them in their orphaned state.

Chris Day 06:04, 29 January 2009 (UTC)

Thanks for pointing them out to me - how can I keep track of such lost pages via a single category or special page? I normally create a stub for the articles on which I collect references here but sometime the server is too slow to really go through the whole page creation process. So these ones are back on my list now, and I will create those articles during the next week or so. --Daniel Mietchen 09:55, 29 January 2009 (UTC)
This category should have most of them (Category:Orphan subpage). Note though that many listed in there will be "fossil" pages, ones that had the template but do not any longer. This is one of the problems with adding categories with the subpages template. While the categories on each page are always current the presence of an article on a category page depends on a recent edit; the categories don't register correctly unless there is an edit to the page. Thus, the list of articles in any category can become outdated quite fast if pages remain unedited. It's a real pain and makes categories somewhat problematic for maintenance tasks. Chris Day 16:17, 30 January 2009 (UTC)

Please note my posting on Talk:Concentration (chemistry)

Daniel, I would very much appreciate a response to my posting at Talk:Concentration (chemistry). Thanks in advance, Milton Beychok 19:17, 30 January 2009 (UTC)

Kugelfunktionen

Daniel, I know that WP.de calls these functions Kugelflächenfunktionen, but I have here Courant-Hilbert, Methoden der mathematischen Physik, Band I (Heidelberger Taschenbücher 1968). On p. 270 we find the Schwingungsgleichung with solution Ansatz u(r)Y(θ, φ). Then a few lines down: nur für die Werte k = n(n+1) genügt werden kann, und zwar durch die Kugelfunktionen Yn(θ, φ). The term Kugelflächenfunktion appears once (p. 274) in Courant-Hilbert (and Kugelfunktion very often), and this flächenfunktion is on a beliebiges Gebiet auf der Kugeloberfläche (not on the whole surface). In addition, I own a German translation of Edmonds: Drehimpulse in der Quantenmechanik (Hochschultaschenbücher 1964) where on p. 31: Die Ylm sind somit die Kugelfunktionen. --Paul Wormer 08:47, 5 February 2009 (UTC)

I had not checked WP on this one but I know both terms are in use, even though most references I read on them were in Engels. In a German phrase, one could indicate the existence of the two terms by writing "Kugel(flächen)funktionen" but this would probably be irritating here. So I changed it into the one that I think is more specific (there are other, though rarer, uses of "Kugelfunktion") and more frequently used in this context. If you're not satisfied by that, I would suggest to use the term employed in the German translation of Landau/Lifshitz (don't have it at hand but could drop in to a library somewhen during the next few days). --Daniel Mietchen 17:35, 5 February 2009 (UTC)
Why would a translation of Landau-Lifschitz be better than the German of two famous Göttinger mathematicians, Courant and Hilbert? Their book was the Bible for all early quantum mechaniciens, including Landau no doubt. The book has an enormous prestige, for a large part due to Hilbert's prestige of course. Anyway, I would be surprised if the translator of Landau-Lifschitz would not use Kugelfunktion. In any case the translator of Edmonds uses it.
I looked at yet another German book (H. Teichmann, Vektor und Tensorrechnung) and Teichmann uses Kugelfunktion for what I would call irregular solid harmonic (power rL+1 in the denominator) and indeed Kugelflächefunktion for spherical harmonics.--Paul Wormer 18:01, 5 February 2009 (UTC)
I do not feel competent to judge whether any of the two books is "better", since I only know one of them. Anyway, I'm in the library right now. Kugelfunktionen is used in Landau/Lifschitz (Band 3, Quantenmechanik) and five of the six other quantum mechanics text books available here (the exception being the translation of Cohen-Tannoudji/Diu/Laloë). Math books (checked about a dozen) usually give both terms, redirecting Kugelflächenfunktionen to Kugelfunktionen. The latter term seems to be used in several contexts, e.g. Kugelflächenfunktionen vs. räumliche Kugelfunktionen. However, such fine distinctions are probably not relevant to our article in question, and so I have changed it back to Kugelfunktionen. Thanks for checking! Groetjes --Daniel Mietchen 19:36, 6 February 2009 (UTC)
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