User talk:AFriedman

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[edit] Welcome!

Welcome to my Talk Page. It's quite active, so you might want to look at the archives.

[edit] GPCR Project

To Graeme: Cool! Where is your book and how is it going? At the moment, I've been focusing on the Gene Duplication Project started a while back. I'm trying to finish as much as I can before school starts, so that is taking up my time--the time that isn't being spent on administrative stuff like getting vaccination forms in order and registering for classes, etc., etc. By the way, I would very much appreciate if you found the online sites where I can download complete genome sequences. A place to start is National Center for Biotechnology Information. I'm especially interested in the genomes of species that were not studied by Fredriksson and Schioth 2005. --AFriedman 15:51, 1 September 2009 (UTC)

Ok, so the species that Fredriksson and Schioth (2005) studied were:

  • Mouse
  • Human
  • Takifugu Rubripes
  • Danis Rerio
  • Caenorhabitis Elegans
  • Caenorhabitis Briggae
  • Drosophila Melanogaster
  • Anophales Gambiae
  • Aribidopsis Thaliena
  • Dryza Sativa
  • Schizosacharomyces Pombe
  • Sacharomyces Ceroversiae
  • Plasmodian Falceparesia
  • Ciona Intestinalis
  • Ciona Savigriyi

Note no results were reported for the last two. I think they were used as controls are they perhaps parammecium?--Graeme E. Smith 03:03, 2 September 2009 (UTC)

Some species that are complete enough to show up for COR include:

  • Encephalitzoon Curiculi
  • Pan Troglodytes
  • Canis Familiaris
  • Rattus Norvegieus
  • Magnaporda Grisea
  • Neurospral crasia

Some species that have got past build 1 include:

  • Plants
    • Populus trichocampa
    • Vilbis Vinifera
  • Algae
    • Chalmydomonas reinhardti
    • Ostreococcus Fucinarius
    • Guillardia Theta
    • Hemistonia andersonii
  • Moss
    • Physocomitrella Pateus
  • Insects
    • Acythosiphno Pisen
    • Apis Mellifera
    • Drosophila pseudoobscura
    • Nasonia vitripennes
    • Tribdium Castanean
  • ehcinoderm
    • strongylocentrofus purpuratus
  • Chridaria
    • Hydra Mangipapillata
  • Protozoa
    • Babesia Bovis
    • Cryptospandium hominis
    • Cryptospandium parvum
    • Dictyostellium discoideum
    • Leishmania Braziliensis
    • Lieshmania infantium
    • Lieshmania major
    • Parmecium tetrarella
    • Plasmodium Falciparia
    • Plasmodium Yoelii
    • Tetrahymena Thremaphila
    • Theileria parva
    • Triconas Vaginalis
    • Trpanonosom Brucoi
  • Marsupials
    • monodelphia domestica
  • Monotremes
    • Omithorhynchius anatinus
  • Other mamals
    • Bos Taurus
    • Equus Cabellus
    • Sus Crofa
  • other vertebrates
    • Gallus Gallus
    • Taeniopygia guttata
  • some species I forget which genus they are in Yeasts?
    • Aspergillus Clavitus
    • Aspergillus Fumigatus
    • Aspergillus Niger
    • Candida Glaborata
    • Cryptococcus necformana
    • Deberyomyces hansenii
    • Eremythecuim gossypi
    • Gibborella zeae
    • Kluyveromyces Lactis
    • Neurospora Crassa
    • Pichia stiptis
    • Ustilagomaylis
    • Yanowia liptyfica

My spelling is probably attrocius, I was scribbling on a loose leaf of paper and I couldn't read my own handwriting.--Graeme E. Smith 04:24, 2 September 2009 (UTC)

Thanks so much! Wow. Let me answer your questions and discuss this. The Ciona species are actually marine invertebrates (sea squirts to be precise, which means they are a very unusual group of creatures arguably in the same phylum as ourselves) and that was a great question about them. There were results in Fredriksson and Schioth (2005) about the Ciona genomes--for example, there were many fewer GPCR genes in Ciona than in, say, humans and a couple gene families had evolved in chordates since the split between Ciona and the rest of the chordates. Were you meaning to ask something else when you said the Ciona genomes hadn't been reported? Perhaps you meant about the non-animal species you'd listed above the Ciona. There were no paramecia in the Fredriksson study (paramecia are a very specific taxon anyway) but there were representatives of Kingdoms Plantae, Fungi and Protista. Of course, for the non-animal species, many fewer GPCRs were found. Maybe from your point of view it isn't "of course," but the proteins from GPCRs are often expressed in the brain.
I have a couple questions myself. What is COR? What URL(s) did you get your list of species from? I notice it's not a complete list of species. For example, I remember when the genome of the sea anemone Nematostella vectensis was published a couple years ago. I don't see that genome in the list of species you gave me. For your interest, the genomes of unusual invertebrates may be the best for my purposes. They often aren't as well studied as the vertebrates, and given the fact that they have nervous systems whose structures can be quite different from those of well studied species, their GPCR families may show unexpected distributions. It's very cool to be able to discuss this with you. --AFriedman 03:59, 3 September 2009 (UTC)

I thought I had already responded to this, but perhaps it got lost in the editor.

My assumption was that species with a build number were considered completed so I ignored the species that didn't have a build number. This information was available from PCBI just in some of the specialized databases associated with it. As for COR, I really don't know what COR is, but it can't be done until the genome is completed supposedly, so those were my first choices. The list is not meant to be exhaustive as much as to indicate which species NCBI thought were complete according to my admittedly naive reading of the database info. I think most of the data came from the gene map tool, but I can't be sure I remember it exactly.--Graeme E. Smith 05:47, 3 September 2009 (UTC)

Hi, Thanks so much! I'll try to get to this when I can. --AFriedman 23:01, 7 September 2009 (UTC)
Okay, I'm here. PCBI: That's the Penn Center for Bioinformatics at the U. of Pennsylvania. Are you sure you mean that, or the NCBI (National Center for Biotechnology Information)? Would it be possible to give me the specific URL where you found the list of species? Better yet, do you have the URL of a nice reliable sequence of the human genome? --AFriedman 15:24, 9 September 2009 (UTC)

Sorry I used the URL for the National Center for Biotechnology Information site. All this alphabet soup gives me indigestion. If you look at the main page (That you gave me the URL for) there is I believe a number of side buttons including one for updates on the current state of the human genome, there being 3 or 4 different genome sequences to choose from. I believe that these different sequences reflect a couple of different subspecies or families of humans that reflect different ethnic somatypes, but I could be wrong. I believe once you know the name of the file, which you can find via the database, you can order the file from ftp.ncbi.nlm.nih.gov

Thanks. In terms of humans, we haven't divided living humans into subspecies and in fact, the species is quite genetically homogeneous. For example, chimps in the same group may be farther apart from one another, genetically speaking, than the two most divergent human groups in the world. It's believed humans descended from relatively recent common ancestors. --AFriedman 22:17, 9 September 2009 (UTC)

That may be, but one reason that DNA sequencing is done, is when there is evidence of families of some small change from the normal DNA sequence, and they want their differences cataloged for some reason. An example is that one family that has lost most of the capability of speech. This is obviously an important reason to check to see what particular illeals they have that the rest of us that speak don't. A corporation for instance might want to copyright that particular set of Illeals so that they can sell kits to scientists that want to study DNA's relationship to speach. I understand something like that has been tried.--Graeme E. Smith 00:54, 10 September 2009 (UTC)

I think you mean "family" as the individuals that are related to a particular person, but "family" is also a taxonomical term for the species that are related to a particular species. For example, there is the dog family (Canidae), the cat family (Felidae), the deer family (Cervidae), the crow and blue jay family (Corvidae), etc. Just to give you a heads up. --AFriedman 21:25, 10 September 2009 (UTC)

Well, yes, that is exactly what I meant.... silly me, you keep expecting me to think like a biologist! --Graeme E. Smith 23:25, 10 September 2009 (UTC)

Are you familiar with the materials in the Introduction to Taxonomy resource over here? Actually, you could go over the materials by merging that page with Introduction To Taxonomy. --AFriedman 16:30, 11 September 2009 (UTC)

[edit] Computer Science

Hello, its good to see there are still a few people around who are contributing to the field of computer science in this section of wikimedia. I have recently joined and have a passion for computer networking. At the same time I would also like to contribute to the perfection of computer science on this wiki. If there are any projects that I could work with you on I would be glad to see if I could help out. Lysander89 12:39, 25 August 2009 (UTC)

I read your userpage and wholeheartedly agree with what you wrote about the need for more activity on Wikiversity. In my experience, many of the learning resources are partly developed by the occasional enthusiastic person who comes along, but rarely used. Perhaps we could start small and simple first, and create a way to teach and certify people in a few basic computer skills. My thought was to model something like this after WikiEducator's Learning4Content workshop, which is a free mini-course in how to use the wiki markup language. If you're really working with a live group of people, that could only help. What do you think? --AFriedman 15:48, 25 August 2009 (UTC)

[edit] Graeme's Latest Book

I am working on a book, called "A New Glimpse of the Brain" and I am some 50+ pages into the data dump version. It is integrating my memory model, and mind model with my new 10 phase Attention Model in an attempt to update my basic theory to include the information I gleaned from Hiedo Braaks book.--Graeme E. Smith 23:12, 7 September 2009 (UTC)

How is it going? --AFriedman 12:38, 9 September 2009 (UTC)

Not especially well, I think there is a memory leak, in one of the programs that I just updated, because when I leave them on too long, I suddenly get a computer freeze, and I can't save my work. The last time that happened despite automatic updates it ate 10 pages of my book. grrrrr.--Graeme E. Smith 14:01, 9 September 2009 (UTC)

Well, these things happen but I know you've been working hard. --AFriedman 15:25, 9 September 2009 (UTC)

[edit] Genezistan's visit

Hi,

Thank you for the greetings. I wonder if I start uploading a resource the size of about a hypertext book on an ongoing basis. will my pages be protected? Regards

--Genezistan 17:43, 11 September 2009 (UTC)

What type of resource are you planning to upload? Which pages are you asking will be protected? Unless the administrators change the settings otherwise, users are free to modify text on Wikiversity but the information will always be stored in "page history." In my experience, unless someone does something egregious pages don't tend to change a whole lot in a short period of time. --AFriedman 18:17, 11 September 2009 (UTC)

I have a lot of unedited text that I need to put in an appropriate form. I thought of a hypertext book format, but I am still experimenting with the various options to structure my materials. Currently, I am engaged in the specification of my subject matter under REFLECTIVE THINKING. All suggestions are welcome. --Genezistan 05:19, 12 September 2009 (UTC)

Is it original research, or is it work on existing research that you can document the original research that it came from? One of our sister projects Wikibooks, is oriented around developing text books but they are not at all happy about original research. The other thing, is do you want to retain authorship? Publishing on Wiki's usually extinguishes some of your authorship rights, to increase the rights of others to use your work. This is necessary because someone just editiing your text for spelling errors has in essence created a derivative product, and has some rights of authorship as a result. Wiki's involve a community effort, where editing of your work is expected. Though not nearly as much of a hotbed as Wikipedia for editing, Wikiversity users will find that random edits have been done on their pages, often only minorly improving them, and sometimes vandalism is done and has to be reversed. You can watch over this by setting your preferences (The preferences button is up on the top line of every page) so that the watchlist includes everything you create, edit, or move. Because of this, if you monitor your watchlist, you can usually see the changes in your data as they happen and determine for yourself if they are beneficial or malign. However because the community is a collaborative community, you might find your data being changed in ways that you do not like. At times this devolves down to reversion wars where people try to protect their own version of a page against another. Because the editing person has rights too, this is counter productive and frowned on by the Wiki-community. If you document your changes of others editing, and discuss why you make those changes on the associated talk page for the page you are editing, you can often head off a reversion war and turn it into a discussion, and possible later collaboration or fork of the page that takes care of your reasons for rejecting the edit. Although Wikiversity is not oriented around publishing, one of the reasons it forked from Wikibooks, is the issue of Original Research, so I think there is an intention that at some level it will be possible to publish here.
As someone who is active on both Wikibooks and Wikiversity please contact me, if you want to discuss the nature of Wiki publishing.
There is another factor you should understand, and that is the upload limitations of Wiki's. Because of the support of the FreeSoftwareFoundation in the early development of Wiki's, there is a tendency to demand that data be uploaded in a format that is not a proprietary file format. This means that most word processor data files are not allowed to be uploaded. It is possible to upload PDF files, as images of your text processing files, but those are not editable being in essence an image of the file. If your stated purpose is to upload reams of text files and edit them into some web-ready form, Wiki-language might be the answer, but how you upload them might be the question.--Graeme E. Smith 14:13, 12 September 2009 (UTC)

[edit] Follow up

Thanks for contacting me again. I have decided to use Wikiversity and I have created two entries: Multidisciplinary Studies and Reflective Thinking. None seems to have read or commented it as yet. But it would be nice to see/read some reaction before I go any further. Regards, Genezistan 07:48, 20 October 2009 (UTC)

I've looked at your course materials (the two pages with the names you wrote above)? I think they are very valuable contributions to Wikiversity. I suggest you get in touch with the people involved in Wikipedia's w:Wikipedia:WikiProject Philosophy and the several Wikipedia WikiProjects that begin with "WikiProject Education." WikiProjects are not solely dedicated to improving Wikipedia but also extend to other Wikimedia projects, even though many people act otherwise. Perhaps you would be able to bring the Wikipedia content developers over here, where they can create different types of resources. In terms of people finding the projects, multidisciplinary studies are also known as "interdisciplinary studies" and are related to the concept of w:consilience. An especially strong section is your description of the problems that need an interdisciplinary approach. I couldn't understand the rationale behind your reflective thinking page as well, and perhaps you could write a similar section in that page (why people need reflective thinking). --AFriedman 02:55, 21 October 2009 (UTC)

[edit] Glimpse is going into its second draft

Hi Anne, I thought I would drop you a line, and let you know I haven't forgotten you, I just got really busy, what with the program I am taking 4 days a week, the club I formed on the 5th, and my own research, which I cramp in edgewise wherever I can. One aspect of my illness that I am looking at, is the loss of function, associated with my mental health, a problem that is cumulative and can be either blamed on stress, or psychosis. (some disorders suggest there might be a relationship where high stress creates psychosis). Anyway, knowing your interest in DNA, I wondered if you were at all familiar with the 200 locations in the human genome that are repetitive, suggesting the need for multiple copies of a single protein. Evidence seems to suggest that the extended time such sections of DNA remain unzipped, makes them more prone to deletions and duplications. In a current model of Autism, it has been proposed that these proteins might have a regulatory role, and that therefore if there is a duplication or deletion the biochemical pathway they regulate, may quit working. If this is true for all of the 200 locations then they may offer us a unique peak into up to 100 diseases, many of which are polygenetic, and therefore translate out into spectrums of similar diseases, that depend on different genetic errors many of which are single point mutations, but which have a low risk factor on their own, but which can in combination cause a major disease. I really like the Stanford Laboratories approach to finding treatments, they have been really effective at finding treatments for the Autistic Spectrum Disorders Fragile X and Rhetts syndome, and have a hope of stretching that success into other disease mechanisms of Autism. I wish the MIT center was as far along, as they are studying a disease that my symptoms are related to the Bipolar and Schizophrenic Spectrum.--Graeme E. Smith 02:16, 25 November 2009 (UTC)

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