Code center > Suggestions
Centromeres in Chromosomes in DB
Numsgil:
I've been working on this one for a while. I view it as the first step in making sexual reproduction a more realistic possibility. By itself it has no real worth (as evidenced by the fact that the number of chromosomes an organism has is in no way reflective of how advanced it is).
The only problem I haven't solved yet is how to create centromeres between chromosomes. (edit: okay, telomeres and oris I haven't decided are necessary or not yet.) I'd like to have the process be:
* somewhat spontaneous
* more likely to, but not exclusively so, occur between identical strands than two entirely different ones
* be somewhat epigenetic.The above list is how actual centromeres seem to work. In any system we come up with, we have to be able to seperate chromosomes paired together (meiosis) and recombine different chromosomes with the same centromere signature.
Real centromeres seem to be somewhat linked with alpha-satellite DNA (long, repeating patterns of Junk DNA).
This is what I was thinking:
Two chromosomes may spontaneously develop a centromere if they have a large area of identical, repeating DNA patterns (an alpha-satellite). The more repititous and shorter this pattern, the more likely it is to occur.
Something like
add sub 4 > add sub 4 > add sub 4 > add sub 4 > add sub 4 > add sub 4 >
in two seperate chromosomes may spontaneosuly connect with each other and form a centromere.
add add add add add add add add add add add add add add add add add add add add
will almost certainly develop a centromere, and very quickly.
I haven't worked out what kind of function will determine the liklihood yet.
Centromeres will be defined as a number. Like numbers stick together, unlike numbers don't.
After a centromere has formed, it will stay in that portion of the DNA forever more ( or until it spontaneously dissapears or something, I'm not sure yet). I'll have to find a way to record it in the DNA but keep it from mutating (that centromere is a physical attachment to the DNA strand, not DNA itself). If the alpha-satellite DNA disappears, it will continue to have a centromere where it used to be. (This is the epigenetic aspect).
During reproduction, if a chromosome has more than one centromere, then it will break into different chromsome strands (where the breakage occurs is random), with each centromere forming it's own chromosome. Then, if a chromosome has a centrome, the chromosome it was attached to has a more or less guarenteed chance of arriving in the opposite cell that it does. Chromosomes without centromeres have a 50/50 of going into either cell.
That is, if a cell has:
1-1 2-2 3 3, where - is a centromere and numbers are each a seperate chromosome strand, and it reproduces, then the two daughters can look something like:
1-1 2-2 and 1-1 2-2 3 3 3 3
Later, I can add a crossing-over, and other chromosomal 'mutations' between chromosomes. Crossing over will help keep chromosomes largely similar, and help decrease the liklihood of centromeres forming on a chromosome that already has a centromere.
shvarz:
OK, let me think about it. Aside from simulating reality, are you expecting some important role for centromeres? Are you suggesting that when (and if) chromosomes are implemented, then by defalt they will be separated randomly into off-springs? That's gonna cause some problems...
Meanwhile, here is an actual scientific paper on centromeres and on their evolution: http://darwinbots.com/centromere%20evolution.pdf I looked over it briefly, it sounds interesting and not too technical. Read it yourself or wait till I read it (over weekend?) and summarize. The best thing about this paper is that the guy that wrote it works next door to me (almost), so I can always go bug him about this stuff :)
Numsgil:
--- Quote ---OK, let me think about it. Aside from simulating reality, are you expecting some important role for centromeres? Are you suggesting that when (and if) chromosomes are implemented, then by defalt they will be separated randomly into off-springs? That's gonna cause some problems...
--- End quote ---
Hmm.. you're right. You need to be abel to ensure that your DNA gets correctly segregated into daugher cells, centromere or no.
Perhaps crossing over is only possible between chromosomes joined by a centromere? Certainly you can't pair up if you can't find each other.
But there also needs to be some way for two identical copies of the same chromosome to end up in the same cell, or centromere's can't form. So perhaps some kind of general reproduction related commands:
1. Copy all chromosomes.
2. Perform X Crossing over event(s).
3. Divide into two daughter cells. (spliting DNA copies equally if there are enough copies to do so).
4. Fuse with another cell (pooling all DNA together).
Our current .repro would be 1 followed by 3. Just doing 3 results in haploid cells if you were diploid, or seriously messed up or empty cells if you were already haploid.
4 lets you model some organisms like hydras, where one generation is haploid, then another diploid.
So we can let cells mix and match what they want to do.
shvarz:
I looked over that paper - you don't really need to read it, it actually deals with a very specific phenomenon in which we are not interested right now. One good thing I learned from there is that the repeatative nature of centromeres is a by-product of that process in which we are not interested. So, don't get stuck on creating repeats - it will have no functional significance in DBs.
What we need is a flexible way to designate which chromosomes are "the same". It should be evolvable. And it should allow many chromosomes to be "the same", not just two.
One thing that we need to take into account is that our chromosomes recombine before we have sex. That is we have two chromatides - one from mother and one from father. But they don't recombine in us. We pass the recombined version to our kids. When bacteria have sex, they recombine their own chromosomes with somebody else's chromosome. The result is immediate.
I think we need to implement only one way. Two different ways to have sex is one way too many... (Never thought I'd say this :) ) So I think we need to recombine DNA right before a new baby is born and we need to recombine mother's and father's chromosomes, not two chromosomes in the same organism. And the mechanism should be in general the same for organisms that are haploid and diploid and polyploid. It should all work through one general scheme.
Numsgil:
Here's what I was imagining:
Two cells tie together. Depending on a macro/micro flag in the options panel:
1. Micro:
Each cell sets .fuse to a positive number (or perhaps non zero to work well with the macro version below). The cells then combine into each other, and their DNA mixes. This only happens if they both set the .fuse flag.
Also, when you reproduce asexually, you have the option to form 2 haploid cells instead of 2 diploid cells (assuming you were diploid).
This way you can model organisms like hydra and some molds, where alternating generations are haploid/diploid.
2. Macro:
Each cell sets a .sperm flag (which can have the same physical address space as .fuse) to a negative number to accept the other cells sperm, or positive to send sperm. Sperm being defined as a haploid set of crossed over chromosomes (crossed over from your own diploid set).
When both .sperm sysvars are non zero, the action attempts to occur. If the correct one negative and one positive event occurs, then the next time the 'female' .repros, the result will be a baby with the father's crossed over DNA mixed with a crossed over set from the mother.
So the 4 reproduction mini commands are just the pieces the larger axexual and sexual reproduction methods are constructed from.
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