GOO Events/Flower Talk Lesson 3

Lesson 3 Log

This was the log for Lesson 3 Orchid Genome Theory and Overlapping Gene Sets

GOO Guide to Genetics Lesson 3

Dreasimy: ~~~Welcome to Class Everyone!~~~ Dreasimy: Ariella, Pascalito, please proceed :D Ariella: http://www.atitd.org/wiki/tale4/Flower_Genome_Theories#Sea_Lily_Genome_Theory Ariella: If everyone would go to that link please and then scroll up to look at the orchid theory page. Ariella: Let me know when you are looking at that page. AliceBlue: hi Ariella and Pascalito. yep got that page up Dreasimy: ditto :D Ariella: We have gone over gene sets and what they do. Can someone tell me what a gene set does? AliceBlue: controls colours size and fert amounts Ariella: That's pretty correct but specific. If you were defining then that would leave out the amount of flax produced or how much maximum color stat in a tend. Ariella: Gene sets control aspects of plants. AliceBlue: ah ok was thinking about flowers :-) Ariella: Someone tell me (by looking at the orchid fact page what the gene set GGG would do on an orchid? Ariella: Yes Alice :) And I hear that alot. That most players think genetics is only about flowers. It is about flax, wheat, vines, anything cross breedable. Pascalito: hopefully papy and veggies next tale :) AliceBlue: papy wow thats revolution, did we rebel? hehe Ariella: Anyone have an answer for my last question? Dreasimy: I want to say GGG makes something yellow but that can't be right as Im looking at orchids with GGG in the gene thingy and these flowers dont have yellow, that I can see blondie: *pictures ooodles of papy* AliceBlue: maybe GGG would give green lower petals? Pascalito: it is correct Dreasimy Pascalito: now what does it make yellow ? AliceBlue: ah yes G= yellow Dreasimy: like aliceblue I would have said lower petals Ariella: a gene set of xxx (three of the color code genes) color the orchid lower petals Ariella: Notice also that the color key only uses coloring of flowers from the primary colors...which are? Dreasimy: CMY? Cyan Magenta Yellow? Ariella: Yes :) Ariella: And I think there is an oddity with orchids and gene sets AliceBlue: doesn't seem any fert amount type gene set? Ariella: As far as I know orchids are the only flowers that can color the same area of the flower (the lower petals) with two different gene sets...which are? Pascalito: correct Alice Pascalito: Orchids are blazing fast splitters, all of them Ariella: Only lilies have a fert amount gene set...the V gene set Ariella: Does anyone see what two gene sets color orchid lower petals? Please use the variable x when you tell them. AliceBlue: can't quite see about two sets for lower petals? Dreasimy: is it xxx and URx? AliceBlue: ah yes xxx and URx Dreasimy: sounds dirty Ariella: See the heading "Color gene sets:" and then look at the end of that group Ariella: Any of our quiet readers who can answer? Ariella: yes that is right alice :) Ariella: Now what gene set colors the upper petal? AliceBlue: Rx Ariella: your basic prescriptoin ;) AliceBlue: lol Ariella: This gets into something more advanced and fun....besides having x-rated and pharmacy drugs Ariella: We can overlap gene sets. Ariella: Let's see if someone can put two and three together. AliceBlue: Are ther only three positions in the gene set? Dreasimy: would that mean there isn't a line between where the left split parent ends and the right split parent begins? Ariella: If you wanted to color both the upper petal and the lower petals but only use 4 genes to build the two overlapped gene sets, could someone tell me what that would be? Pascalito: The line of the slice is virtual, the hybrid does not *se* that line AliceBlue: no, lost now Ariella: yes there are three positions in the lower petal gene set. Dreasimy: except for the size gene sets? Pascalito: *see* Ariella: Dreasimy, I'm not sure what your question above means. Are you talking about the child flower genome? Pascalito: even then, if RO comes from left and YG from right, you have a giant Dreasimy: ya but no worries I was just guessing at the question :D Ariella: At this point we are talking about gene sets in general. So Rx would color the upper petal. xxx or URx would color the lower petals. AliceBlue: Not quite sure what the U and the R are meaning? Ariella: You can overlap gene sets. What is that pencil puzzle game that you can find hidden words inside of a block of letters? Pascalito: just controlling genes, like any letter in a word, and not variable like x (x determines the color) Ariella: Remember in lilies that Uxxx...the U meant the xxx color would color the inner petals. AliceBlue: ok Ariella: If we capitalize a letter gene in a gene set then it is static and has a definite control over an aspect of the plant. Pascalito: You will notice that the very short gene sets in orchids allow for loads of colors in very few genes:) Dreasimy: so, Rxxx could color both sets of upper and lower petals? because it contains Rx (upper) and xxx (lower)? AliceBlue: so you get xxxx for that overlap? Ariella: Dreasimy that is correct :) AliceBlue: ok Ariella: There is also another overlap of only three gene letters...URx. Pascalito: another small example: what would this sequence of genes cause: YUROO ? Ariella: URx would color the upper petal and the Rx part would also color the lower petals Ariella: What is that pencil puzzle called that has hidden words in a block of letters where you circle words that can be found diagonally, vertically or horizontally? Pascalito: Hint: those 5 genes contain 4 gene sets... Dreasimy: yellow leaves and cyan main petals? since xU is now Yellow U (leaves) and Rxx is now R cyan cyan (main petals)? Ariella: yes Dreasimy :) AliceBlue: In YUROO are you calling variables? Pascalito: YU is magenta leaves btw Ariella: Is everyone familiar with that pencil puzzle? That is what looking at a genome is like. AliceBlue: or is it part of the size? Dreasimy: oh right oops that Y gets me every time :D Ariella: xURxx is the format alice Pascalito: yup, was same for me after lilies Ariella: So you would find xU and URx and Rx and Rxx gene sets in that sequence AliceBlue: cyan main petals and magenta leaves Ariella: Why is this important that gene sets can overlap? Dreasimy: the pencil puzzle I think is what I'd call a word search but maybe there's another name for it :D Ariella: I'll answer my question. Dreasimy: good cuz I have no idea :D Ariella: Genomes have lengths. So if you know how to overlap gene sets then you cram more 'stuff' happening into that genome. Ariella: Genomes are not static however, like we saw in the advanced cross breeding where we figured the length of the child flower. Pascalito: you cannot even avoid some stuff from happening, take ROYG for instance... AliceBlue: does any of the overlap mean you get a stronger colour? Pascalito: repetition gives stronger color Pascalito: overlap makes it often easier to combine things Ariella: Alice, only if you can cram more gene sets in, then you can get more layering of color on a certain area of the flower. AliceBlue: ok, yes repetion like on the lillies Ariella: Does anyone have any questions about the overlapping? Dreasimy: so basically your individual gene of R or O or whatever can participate in 2 gene sets and getting that right can maximize your output of manageble characteristics? Pascalito: ROYG (giant gene set) ALWAYS has RO in it of course, RO meansCyan Upper Petal ! Dreasimy: ahh Ariella: To make sure everyone understands about shades of color and gene sets... yes, Dreasimy, good way to put i. Pascalito: just like Rxx also has Rx in it, always; no way to color main petals without coloring upper petal :-P Dreasimy: ahh :) Ariella: We see that Ux colors the stem. Looking at the color key we see that if we use O for x and have UO in a gene set then the stem is colored what color? AliceBlue: cyan Ariella: yes :) So if have Ux and Ux as UO and UG what color would the stem be (hint: think of a secondary color we talked about)? Ariella: If we have those two gene sets somewhere in the genome, that is Dreasimy: well cyan and yellow make..... Dreasimy: green? :D Ariella: right :) What if UOUG were right next to each other in a genome? What parts of the orchid would be colored and what color would each part be? AliceBlue: stem green leaves cyan Dreasimy: I agree on stem but I thought leaves yellow Ariella: O in the color code is cyan. OU Dreasimy: I think i messed up Dreasimy: hehe AliceBlue: getting the hang of the variables Dreasimy: good job AliceBlue :D Ariella: If you do like the word search then you could circle these gene sets...UO, OU and UG. Since UO and UG both color the stem then you have color layering to think about too. AliceBlue: so the OR in dwarf could be overlap with xR of front petal where x = O Ariella: One last test on gene set overlapping...YUROOOU Pascalito: yes, dwarf always does cyan front petal shade Ariella: yes it would alice :) Ariella: separate out the gene sets first, then tell the area of the orchid and colors. Dreasimy: Ok so YU URO RO OOO OU = YU Magenta Leaves + OU Cyan Leaves = Blue Leaves? and then URO Cyan lower petals + OOO Cyan lower petals = really cyan lower petals, and RO = Cyan upper petals, and ROO = cyan main petals? Dreasimy: oops forgot ROO in my gene sets Pascalito: excellent !!! Ariella: yes that is correct :) Ariella: I just wanted everyone to have some examples so that they can go back and look at these as reference. AliceBlue: will have to sort that out later, got lost on that one Ariella: Also, now that you see how overlapping works, let's go back to cross breeding a minute. Dreasimy: doing the word search thing really helped with that example for me Ariella: good :) Pascalito: we do that all the time Ariella: Look at your orchid child flower that was the homework cross. Pascalito: sometimes other way round when we build gene strings for specific targets Ariella: Maybe this can help explain why your child flower does not necessarily take colors strictly from the parent flowers. AliceBlue: I wrote down your answer Dreasimy! Dreasimy: hehe this will all be on the log too :D Ariella: Where a splice occurs between the two parent genomes it can put together a gene set(s) that were not originally in either parent. Pascalito: Just like I remember Rania having a dwarf lily from parents that had no dwarf gene sets at all Ariella: Btw, in the above example, it would be shade 2 cyan lower petals as Dreasimy put it 'really' cyan lower petals. We abbreviate that as LPcyan2 Dreasimy: okie Ariella: Lower Petals cyan shade 2 Pascalito: You guys remember the max number of shades possible ? Ariella: You remember how we centered the shorter genome of the Left Splint and Right Splint parent? AliceBlue: yes 4 shades Dreasimy: ya this time I put my parents genomes in a spreadsheet and printed them out the bigger one on top Ariella: If the child flower length had been a fraction and you rounded up then you would shift the shortest genome by 1 towards the Splint side it was in. If the shortest genome was on the Left Splint you shift it 1 to the Left over the Right Splint genome. If the shortest genome was on the Right Splint then you shift it to the Right under the Left Splint genome. Ariella: The above is a reminder. Ariella: I'll point out one more difference about sea lilies and orchid gene sets. Ariella: With orchids a giant gene set ROYG and a dwarf gene set GYOR in the same genome would cancel each other out equally in an orchid genome. Ariella: It takes two giant gene sets ROYG+ROYG and only one dwarf gene set GYOR to cancel out and make a normal size flower. Ariella: One last example on advanced cross breeding as a review. Ariella: Sorry, on the sentence above I meant a normal size lily. Ariella: Let's pretend we have two parents with very short genomes. Left Splint UROOO and RO. Ariella: RO is the Right Splint genome Ariella: UROOO with RO centered underneath. But you see that RO does not center. You need to shift RO by 1 gene in which direction? Dreasimy: right, since it was in the right split so it gets moved 1 spot toward the direction it was the split of... AliceBlue: to right Dreasimy: we both get a cookie! (I hope) Ariella: Excellent :) AliceBlue: hehe Ariella: So OR lines up under the first OO or UROOO Ariella: chocolate chip...now I"m hungry Ariella: And how long would the child flower be? Dreasimy: 4 genomes? Ariella: the first OO of UROOO Dreasimy: you take the average of the 2 parent lengths and round up? AliceBlue: 4 Ariella: heehee 4 genes, yes Ariella: And where would the beginning of the child flower genome start with? AliceBlue: the U of the parent on top Ariella: and a sentence above should read "So RO lines up under the first OO of UROOO" Ariella: So list some possible child flower genomes AliceBlue: does the last O of the parent drop off because it is beyond the last splice point? Ariella: yes alice Pascalito: just like the UR of the left is always part of the child Dreasimy: It seems like it has to be UROO where only the O of the right split is part of the child Ariella: you always keep the first genes of the longest genome where it has no genes under it from the shorter genome Ariella: Possible child flower genomes... Ariella: URRO AliceBlue: or URR AliceBlue: from first splice point Ariella: UROO where Dreasimy said and also that same genome but it is retaining the last two OOs from the Left Splint or longest genome and no genes from the shorter genome parent. AliceBlue: eeep maybe URR doesn't exist? Dreasimy: ok my confusion is stemming from there is no UR or URR genome? or so I thought :D Ariella: Alice, remember that the child flower will be 4 genes long...5 (left splint genome length) + 2 (right splint genome length) divided by 2 and rounded up to 4. Pascalito: it could technically exist, in the special instance of an eliminated gene (we do not consider those yet really) AliceBlue: ok :-) Ariella: So RO is lined up under the first OO of UROOO Ariella: and the first splice point (or visually the vertical line you draw) would be right after UR but in front of the R in the short genome RO. Ariella: So that could make a possibility of UR-RO Ariella: Basically then number of possible child genomes is the length of the shortest genome parent + 1. Ariella: Dreasimy does that help? Ariella: Which is 2+1=3 Dreasimy: I think, so basically in this case the options for child are UROO, URRO and UROO, because you can get your O's in 2 places? Ariella: URRO Ariella: UROO Ariella: UROO Ariella: yes :) Dreasimy: I got you homie :D Ariella: yo, high five! AliceBlue: but that is length of shortest plus 2? AliceBlue: oops forget I said that AliceBlue: confusing amount with length sry Ariella: No, that's okay. Please everyone talk out loud as you think it out. Ariella: I think that is all for tonight unless someone has a question? AliceBlue: I'll think out the word search and chat you if I still can't see it :-) Dreasimy: I guess my biggest question is visually how can I guess if my color difference from parent to child is just more intense shades or a different color adding to it Dreasimy: just deductivly looking at the word search possibilities? Ariella: Yes, anyone is welcome to chat either Pascalito or myself about this stuff. Ariella: Dreasimy that's a good point about color shades. Ariella: We routinely plant new baby flowers beside ones of same shades or near same sizes or we can't tell lol AliceBlue: My flower got hot pink main petals Ariella: And one reminder, there could also be the possibility of a subtracted gene or added gene in the example above. Dreasimy: me too Alice way more pink than the hidden in darkness main petals which look kinda red to me Ariella: So some more possible child flower genomes could be... Pascalito: I have also started work on a very long term project: making 125 lilies with all possible colors on middle stamen Ariella: URO Ariella: UOO AliceBlue: why did we want our name on it? Ariella: URRRO Ariella: Thanks, Alice, meant to say why that is important Ariella: UROOO Ariella: Thinking about how important it can be to track genomes and know the possibilities of your child flower genomes... AliceBlue: the homework is max fun anyway even if the lectures are hard Ariella: Someone this week (and many other weeks) asked for advice on the next cross after they used a hybrid flower from someone else. Ariella: If the beautiful hybrid you got from someone else does not have their name on it as a prefix...say Pascarella Pipsqueak.... Ariella: and you forgot who it was from, how would you make an intelligent cross if you did not know which end of the genome the giant set was on? Or the two magenta lower petal sets that made your orchid glow. Dreasimy: you'd... throw some mutagens on them and cross your fingers for awesomeness? :D AliceBlue: LOL Dreasimy: aka you couldnt make an intelligent cross Ariella: It is not vanity to put your name as a prefix. There are very good reasons. Then you could chat that originator of the flower, ask what the probably genomes is and go 'hot dog! that double giant set is on the left side'. AliceBlue: right :-) AliceBlue: mine got giant, did yours too Dreasimy? Ariella: lol awesomeness could take awhile in that case Dreasimy, and cost alot of mutagens ;) Dreasimy: ya Alice :D AliceBlue: ver cool, I called Mine Alice Blue Sunrise Dreasimy: I tlooks almost exactly like Hidden in the Darkness but more pinky purply on the main petals and lower petals Dreasimy: Mine is Hidden in Dreasimy rofl AliceBlue: hahahah Ariella: Alice, because yours got a giant then you at least know that the splice occurred AFTER the giant gene set. Pascalito: giant or not in the homework child is a very good start to eliminate a series of possible splices :) Ariella: lol Dreasimy AliceBlue: ok :-) Pascalito: guess what i just did :-P Dreasimy: discovered the way to crossbreed papyrus? Ariella: And now just look at the color and size gene sets to try and interpret your child flower and where that splice might be. Pascalito: FEEEEEEEERT! AliceBlue: hehe Dreasimy: <ducks for cover> Ariella: Again...if you're super curious...and it's a very gorgeous flower...split it and put two splits in the greenhouse and hit it with solvents. AliceBlue: and beautiful purple upper petal, quite amazing Pascalito: poor fishiess in it... Dreasimy: my purple upper looks the same as the hidden in darkness parent :D Dreasimy: so you musta got an extra shade :D AliceBlue: no think mine is same too, but the front petals went purplish too Ariella: possible you could have an added gene that made added color too AliceBlue: made it look more prple :-) Dreasimy: Ya know GOO likes handing out prizes... so I want to give a gold star out today Dreasimy: In honor of your focused attention and academic achievements, AliceBlue you win a Huge Quartz (aka gold star) :D AliceBlue: hehe ty :-) Pascalito: for builds, we have to do as if doublimg/eliminating genes is not there, but we still have to keep in mind that about 25% of hybrids have an added gene, and 25% of hybrids have an elimitated gene... AliceBlue: Question about future lessons. Are we going to actually make mutagens? AliceBlue: and if so, are there public labs? Ariella: You can, but it's not practical once you realize how to use them. AliceBlue: ok so thats not a homework assignment Dreasimy: last tale I threw mutagens randomly at things and it really didnt help so I probably wont do that again until I learn more :D Ariella: Garden of Eden's main project we work towards is Mutagenics and understanding genetics in general. We are working towards 50 mutagen labs or more and discovering as many mutagens as we can. AliceBlue: hey two hours flew by.... time to FEEEEEEERT LOL Dreasimy: Thank you Ariella and Pascalito so much for another amazing session :D Ill get the log up asap :D AliceBlue: ty too :-) Ariella: Using mutagens is about the most powerful tool in this game. And the most fun :) Those mutagens produced in the Eden labs will go out to those who learn to 'build' and turn in builds. Which means anyone can play with mutagens. Ariella: Thanks y'all :) It's fun to share and see others see the potential in this genetic stuff heehee

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