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The links at the bottom of the Higher Order Visual Perception section contain information I'd like to include in that section.  As is, the section seems a little flat, and needs to be fleshed out a bit more.  You're welcome to read, comprehend, and include any of them if you've got the time.  If not, I'll go through and expand that section later. - Chris 12/4 16:25

I already address Mike's comments on putting in biological chemistry and the direct connection of chomophores  to photoreceptor is what he is talking about with an invertebrate system . The multiple photoreceptor for different wavelength of polarized light is how the see long distance. I did not find that fact but will still do some more searching. 
I done basic seaches and went to the library could not find a  answer on P-vision and navigation with cephalopods lots about use in insects but not anything else will look more Matt
==Comments by Mike==
Looks great folks.  Here are a few general comments and things you might want to address.  I apologize in advance if you mentioned them already and I overlooked them.

the story was funny, you can post it or not, it doesn't matter to me.  Not sure I understand the biological action section in the comparative anatomy.  Can you put this in your own words so that I can understand it?  I could use more of your interpretation of some of the details.  One of the really cool things about cephalopods is that they have vertebrate optical system with an invertebrate photoreceptors (rhabdomeres). You might even want to look at invertebrate wikis for some help with this.  Their retina doesn’t have bipolar cells, amacrine cells, horizontal cells, etc….some can be found in the brain.  they also have very large fibers.

I was under the impression that the lens is pulled back toward the retina for near vision.  Short focal length of lens (wide angle of vision)  and long photoreceptors mean they can see close and far very well!

Two corneal layers????  What about their ability to resolve images.  I was under the impression that they had a low number of photoreceptors (reduced density therefore poor resolution...remember fovea in humans).  True?
They have a pupil...very unusual!  function?
More detail about visual spectrum needed.  475, 490 nm chromophores????…Remember that the ocean acts as a giant filter of light!


love the section on changing colors.  Is the following true?  They can change colors instantly through the release of chromophores by muscle contraction.  Do they do this in response to seeing color?  In other words, is their ability to change color paired with color perception?  Is it purely a reflex that doesn't interact with their brain?

expand a bit on planes of polarized light detection and its use of navigation (again might want to look at flying insects here)
Lots of cool research on Cuttlefish (j.z. young) trained to recognize patterns.  Removed parts of brain to localize function.  any of you encounter this stuff?

Bioluminescence?

==Pre-Comment Discussion==

   the chomophores work one and another that why and was there it can do both at same time in biological systems
matt  12-2
I am a little confused about what is going on with all of the links at the bottom of the higher order visual perception section.  Does somebody need help turning them into citations?  Where do they go?  -Rae 12/2, 22:46

I am trying to work through the Phototransduction in the Skin section, and it looses me a bit in the third to last paragraph. There seems to be fragmented sentences and without more information on what is ment I can not edit it. I will paste the phrases I am refering to on here. It also seems to need some more "dumbing down" but again it is hard to be the one to dumb it down when I am not the one who wrote it.  :)
Although the term "chromatophore" also can refer to colored, '''membrane associated vesicles (organelles) found in some forms of photosynthetic bacteria'''. In addition to their obvious value for the animals with chromatophores, these cells are being explored for potential application for people, including modeling diseases, use in '''appetite suppression and tanning''', ('''and''' <--''delete?'') as biosensors and for rapid disease detection.

I am working on the editing of the page.  I am curious about the "*CITATION NEEDED*"  on color vision.  Who ever did do that section could you please put in the citation.  I am going to remove the note in the actual wiki but I wanted it to still be done.  

Ah!  Excellent!  I'll go through and give *actual* citations instead of links to pdf's. http://en.wikipedia.org/wiki/Help:Shortened_footnotes looks most applicable.  Thanks a lot! - Chris, 11/28, 20:29

I just tried to write out an explanation but it gets messy since the code in my explanation gets turned into a reference.  So, you can find information here:  http://en.wikipedia.org/wiki/Wikipedia:Citing_sources

You can also look at how it has been done in text already.  If you're still not sure, give me your email address and I can explain it to you.  -Rae 11/28, 19:59

I feel stupid for asking this, but how do you add citations? - Chris 11/27, 18:27

Enjoyed this story but thought it was better to keep it out of the material we're turning in.  Want other folks in the group to be able to read it though so moved it here.  Thanks for the entertainment, whomever wrote this :). -Rae 11/28, 17:36

Ocean War 2
Many years ago Butter and garlic got together and declared war on cephalopods. It all started when cephalopods bombed Dairy harbor and killed all the garlic on the waiting battle ships. This woke the sleeping giants of butter garlic nation.
The Nation awoke to the horror of millions threatened and war on the horizon . The Mollusk nation already was at war with the continent of cocktail sauce . The war had gone on for many years and they begged that butter and garlic nation should come to their help. 
When Cephalopods bombed Dairy harbor the whole nation voted to go to war with the cephalopod Island and also their allies Mollusks. After years of fighting the great invasion of Molluska  succeeded and they surrender to the allied nations of cocktail sauce and Butter and garlic. 
The butter and garlic nation then turned to the west ond started the Island hoping campaign of conquest to subdue the island nation of Cephalopod. Using the scientific discoveries of Molluska and its own research, they were able to develop the Boiling water bomb.
Garlic and Butter flew the Enola gay over the island nation and drop the boiling water bomb cooked the whole city in Cephalopod in an instant. The Emperor of Cephalopod surrendered and Butter and Garlic invaded the Island. To this day there is a memorial to the victims of boiling water dropped by Butter and Garlic.



We need citations for the introduction! -Rae 11/24 14:35

I believe there is a chat component available on skype.  When will folks be around?  I can be available anytime tomorrow or Saturday if I know in advance. - Rae 11/24 11:33

Skype would be fine, but I'm (unfortunately) microphone-deficient.  Does Skype allow keyboard-only individuals to join in on conversations?  Or should we use Google Doc's multi-user IM thing I've heard about?  Thanks for creating all the sections, by the way. - Chris, 11/23, 15:13

Also, a lot of the material formerly under "sub heading" (now at the beginning) is not relevant to this project.  Can we schedule a skype meeting or something so we can all get on the same page? (so to speak)  -Rae 11/23

Here is the info moved from the biological chemistry section as found at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1134798/
-Rae 11/23

D-Asp (D-aspartate) is an endogenous amino acid found in the nervous and endocrine system of various animals. It was first found in the brain, stellate ganglia and axoplasm of the giant axon of the molluscs Octopus vulgaris (common octopus), Sepia officinalis (common cuttlefish) and Loligo vulgaris (common squid) [1,2]. Subsequently, D-Asp has been found in the nervous and endocrine tissues of many other animals, including the invertebrates Aplysia fasciata (sea hare) [3], Ciona intestinalis (sea squirt) [4], Penaeus japonicus (Kuruma prawn) and Jasus lalandii (rock lobster) [5] and the vertebrates Rana esculenta (green frog) [6], Podarcis sicula (Italian wall lizard) [7], Merlucius merlucius (European hake) and Solea solea (common sole) [8], Gallus gallus (chicken) [9], Rattus sp. (rat) [10–16] and Homo sapiens (human), in brain [17–19] and in cerebrospinal fluid [20,21]. As far as the physiological functions of D-Asp in the animal kingdom are concerned, important biological roles for this D-amino acid are now postulated for many invertebrates and, particularly, in higher vertebrates. In fact, it has been observed that in the brain of chicken [9], rat [10–12] and human [18], very high levels of D-Asp occur transiently during the last stage of the embryonic life or in the early post-natal life, suggesting that D-Asp is involved in the development of the nervous system in these animal species.
In addition to the role that D-Asp has in the nervous system, other studies have demonstrated that D-Asp also has an important role in the endocrine system. In adult rat, it has been demonstrated that D-Asp has neuronal and neuroendocrine roles [22–24]. D-Asp has been found at very high concentrations in adrenal, testis, pituitary, thymus and ovary [12]. Later, D-Asp was also found in very high concentrations in the pineal gland of rat (approx. 1.0 μmol/g of tissue), with a peak of concentration during the night (2830 pmol/pineal gland) [13,16]. The peak of D-Asp was concomitant with the higher concentration of melatonin in this gland (5.7 pmol/pineal gland), thus suggesting an involvement of D-Asp in the synthesis and release of melatonin [25]. High concentrations of D-Asp in the pineal gland were observed by Lee et al. [26], who also found D-Asp in the pituitary gland and retina [27]. In addition, it has been demonstrated that the pituitary gland has a high capacity to accumulate D-Asp, and that this amino acid has the capacity to induce the release and synthesis of testosterone either through the release of LH (luteinizing hormone) or by acting directly on the testes to release testosterone [22], as well as being implicated in testosterone synthesis in rat Leydig cells [23] and in spermatogenesis [24]. The implication of D-Asp in the maturation of sexual glands and in the synthesis and release of steroid hormones has been demonstrated to occur in the frog Rana esculenta [6] and in the lizard Podarcis sicula [7].
Parallel to the biochemical study, immunohistochemical studies using an anti-D-Asp antibody have also demonstrated the presence of D-Asp in a variety of cultured mammalian cells, e.g. cultured rat pinealocytes [25], pheochromocytoma PC12 cells [28], rat GH3 pituitary tumour cells [29] and pheochromocytoma MPT1 cells, a subclone of PC12 cells [30], as well as in animal tissues, e.g. various regions of rat brain [31,32], rat adrenal gland [33], pineal glands [26], the central nervous system of rat embryo E12 [15,16] cells, spermatids of rat testis [24,34], and rat pituitary and retina [27].
It has been demonstrated that NMDA (N-methyl-D-aspartate), a molecule well known for its neuroexcitatory activity and for its action on the L-Glu (L-glutamate) receptors belonging to the NMDA class, is an endogenous compound that is present in rat nervous system and endocrine glands [35,36]. This compound is biosynthesized in vivo from its precursor, D-Asp, with a SAM (S-adenosylmethionine)-dependent methyltransferase enzyme being responsible for its synthesis [35,36]. Both D-Asp and NMDA are mostly concentrated in the rat adenohypophysis, hypothalamus, brain and testis [35]. It has been demonstrated that NMDA induces the release of GnRH (gonadotropin-releasing hormone) from the hypothalamus, which in turn induces the synthesis and release at the adenohypophysis of LH, GH (growth hormone) [35] and prolactin [36] in rat. This phenomenon, which was based on the mutual action of D-Asp and NMDA in the synthesis and release of nervous and endocrine hormones, has also been demonstrated to occur in the tunicate Ciona intestinalis [4]. Finally, in addition to the release of LH, GH and prolactin, as mentioned above, more recently, D-Asp has also been demonstrated to be involved in the release of α-melanocyte-stimulating hormone, GABA (γ-aminobutyric acid) and dopamine [37]. D-Asp is present in all magnocellular neurons of the rat hypothalamus, and participates in oxytocin production during lactation, as well as increased oxytocin gene expression and decreased concentration of circulating oxytocin [38]. A last interesting observation is that D-Asp has also been found as a nuclear component of cells in the mammalian hypothalamo-neurohypophyseal system, and it is supposed that D-Asp interacts directly with DNA or nuclear proteins to activate/inactivate genes in order to control transcription [39]. A specific mRNA and related protein, steroidogenic acute regulatory protein, has also been demonstrated [40].
A racemase that specifically synthesizes D-Asp from L-Asp, D-aspartate racemase, has been found in rat brain [16] and in the mollusc blood shell Scapharca broughtonii [41], indicating that D-Asp is synthesized in vivo. In addition, a D-AspO (D-aspartate oxidase; EC 1.4.3.1), the enzyme which specifically oxidizes D-Asp into oxaloacetate has been found in various animals, and has been purified from O. vulgaris [1] and from beef kidney [42].
In another set of studies, using an enzymic method based on the use of D-AAO (D-amino acid oxidase; EC 1.4.3.3) and chromatographic methods based on the enantiomeric separation of amino acids with chiral HPLC stationary phases, D-amino acids, other than D-Asp, have been found in invertebrates and mammals, but at very low concentrations compared with D-Asp, except for D-Ala (D-alanine) and D-Ser (D-serine), which were found at concentrations approximately the same as that of D-Asp. In mammals, D-Ala has been reported to be present in human brain [17], in human cerebrospinal fluid [20] and in rat pituitary gland [14]. Other interesting studies have been performed on D-Ser. In rodents and humans, several groups have demonstrated that free D-Ser occurs predominantly in the brain, and persists at high levels (200–300 nmol/g) in embryonic and post-natal life [18,43]. However, while D-Asp was found at higher levels in the endocrine glands, D-Ser was found at high levels in the brain regions (cerebrum, hippocampus and hypothalamus) [18]. In addition, interesting studies have been conducted in rat that demonstrated that D-Ser selectively potentiates NMDA-receptor-mediated neurotransmission at the glycine site [44].
this is just for info now can expand later


Can we please only put our own work on the main page?  It is really confusing having large uncited chunks of material from other sources.  Also, can we please include citations as we go?  It will make things a lot easier later, plus then the rest of us can check out the sources.  Thanks! -rae 11/23

What's the plan? -rae
I am new to wiki and put links up just for info we can put this on main page with cittions that is why I asked for help on citation

== Neural Development ==

hey I'm sorry I do not know how to edit the page and make it look nice. I did the seciton on neural development and I'm not sure what happened but I do not know how to fix it. If someone could please help that would be lovely. Thanks -Molly

==Higher Order Visual Perception==

http://jeb.biologists.org/content/212/14/2133.full.pdf+html
 Do cephalopods communicate using polarized light signals?

http://www.mbl.edu/mrc/hanlon/pdfs/barbosa_et_al_vis08.pdf
Cuttlefish camouflage: The effects of substrate contrast and size in evoking uniform, mottle or disruptive body patterns


http://www.mbl.edu/mrc/hanlon/pdfs/Crook%20etal%20NautilusSpatialLearn%20JCB%202009.pdf
Memory of Visual and Topographical Features Suggests Spatial Learning in Nautilus (Nautilus pompilius)


http://neuromancy.southernfriedscience.com/?p=522