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Author Topic:   How well do we understand DNA?
TheLiteralist
Inactive Member


Message 1 of 98 (177444)
01-16-2005 1:12 AM


Mutations, On-purpose Randomness, & Junk DNA
Some other thread discussions have made wonder some things...
  1. How well do we understand DNA in general? I'm not referring to the human genome specifically. Any genome...maybe something simple like a bacterial genome. Are we able to say, "Okay, if we connect these 50,000 base pairs in this sequence we will get these results?"
  2. Are we certain that all changes in DNA sequences are a result of random mutations--i.e., copying errors? This question is inspired by experiments wherein supposedly one bacterium develops a colony with many variants. How do we know that there is not some method within the genome that is supposed to generate some level of variation--i.e., it's not random mutations but rather variation achieved through randomness generated purposefully by the code? A limited experience in programming has taught me that in many programs it is often useful to have a random generator module. For instance, if I wished to write a code for the game Solitaire, I would, somewhere, have a random generator to come up with the card order. However, the randomness would be purposefully limited in what it could affect. It couldn't, for instance, ever cause the game to become Poker. There would be certain modules that I would not want to ever want to be affected by the random generator, and should something happen (like a power spike) to "randomly mutate" those modules, the program either would not run at all or, at least, would not run optimally.
    Therefore, IF the genetic code is by intelligent design, how would we differentiate between random mutations and purposeful, limited randomness--and has this already been done somehow? (I'm trying to make it clear, but I don't know if I'm succeeding.)
    This idea is specifically pointed at the idea of limits within "kinds" of creatures.
  3. What is JUNK DNA? Another post referred to it as DNA that doesn't regulate or get transcribed. (I have heard, I think, that it is a build up of left overs from ancestors.) Is it possible that this junk DNA DOES perform some function, and we simply either have not observed it as yet or have observed it and didn't know what we were seeing? Could it be acting as a data base for potential features (just an outright guess based on no facts at all)? What have we seen "junk" DNA do or not do that has caused us to dub it as "junk?"
I would particularly like to hear from those whose fields are related to DNA or in some manner. I may not agree with you at all, but I would very much like to know your opinions on the matter as well as the reasons you hold such opinions.
These are areas of genetics I've done no prior study in; so I will likely not be able to debate the topic much (of course, if I feel like I can, I will try).
Also, my background in biology is high school level; so please, if possible, keep things to the layman's level.
Thank you very much.
--TheLiteralist
{edited to add italics to a word--I'm sure it made the OP MUCH clearer!}
{edited again to strike through a couple of repeated phrases (copying errors?...heh)}
{edited...ooh ooh...just noticed the optional Sub-Title...gotta have it}
This message has been edited by TheLiteralist, 01-16-2005 01:13 AM
This message has been edited by TheLiteralist, 01-16-2005 04:04 AM
This message has been edited by TheLiteralist, 01-16-2005 04:06 AM

Replies to this message:
 Message 3 by RAZD, posted 01-16-2005 1:48 AM TheLiteralist has replied
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TheLiteralist
Inactive Member


Message 4 of 98 (177470)
01-16-2005 3:54 AM
Reply to: Message 3 by RAZD
01-16-2005 1:48 AM


Are Mutations Assumed or Proven, Though?
Hi RAZD,
Thanks very much for your reply.
2. We know that some genetic sequences are more susceptible to mutation than others. My personal opinion is that the rate of mutation has evolved to match the need for it by regulating the level of susceptibility. An organism that mutated too much would have trouble finding mates, while an organism that mutated to little wouldn’t have enough variation in the bank to survive natural selection events. It is also logical that if this is the case, that a stressed population can turn up the rate of mutation by turning down the regulating mechanism with stress signals. Again, certain gene sequences could be more affected than others so you would have your random module in the sequences most likely to result in viable variations and less in the ones that would result is non-viable variations.
Of course, I wouldn't expect you to share my views. However, I wonder if you could work, temporarily, from the Intelligent Design premise. I contemplate that somewhere (or many somewheres) the sequences FORCE variation on purpose and in a limited, controlled manner so as to make living organisms both interesting and resilient. And, even, from this view, the Designer would have considered the various stressors of the environment, which He also designed, and so could have made the sequences somehow able to react to triggering stresses.
It just seems like an at least equally valied way of interpretting the whole DNA thing. My knowledge of the subject is so limited, though.
But my question is really: Are mutations assumed or proved? And, if proved, how exactly? Because, I think it would require that the entire code be fully understood in order to prove this assertion. So, if the code is not fully understood, then I don't see how it can be asserted (though it can be assumed) that the DNA variations are resulting from random mutations. I keep hearing "copying ERRORS," but how do we know that those are errors? What if the code is doing exactly what it is supposed to be doing--i.e., creating a certain amount of variation within certain limits?
(I wouldn't necessarily expect you to be able to answer RAZD, though perhaps you can--I'm just really curious about this and kinda thinking out loud.)
Personally I don’t think any DNA is junk, just that the purpose is not known or understood enough. Consider that it takes a considerable expenditure of energy to produce these sequences, and that if they did not serve a purpose that they would be eligible for being weeded out by selection, especially in stressed populations (starving, insufficient nutrients, etc), and that is not happening.
Given the astoundingly detailed ways that nature does things (from either POV), I would consider such a view the logical choice if working from the evolution paradigm. If working, as I am, from the Creation paradigm, then there should be almost, or utterly, no "junk" DNA (some renegade sequences possibly having developed since the Flood due to existence in the wrecked, far-less-than-optimal, no-longer-Edenic environment).
Thanks,
--TL

This message is a reply to:
 Message 3 by RAZD, posted 01-16-2005 1:48 AM RAZD has replied

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TheLiteralist
Inactive Member


Message 21 of 98 (179821)
01-23-2005 12:42 AM
Reply to: Message 6 by Sylas
01-16-2005 4:27 AM


Conserved Sequences
Hi Sylas,
I am thinking of the genetic code like a programming language. So just as a programmer might use a certain code module (for instance, a code sequence that makes highlighted text bold) in many programs; so the Creator might have numerous genetic modules which can be used in many creatures to accomplish similar tasks in all the many organisms.
How can one distinguish between a conserved genetic sequence and a particular genetic module that the Creator might have used in various organisms (to achieve similar functions in various organisms)?
Thanks,
--TL
This message has been edited by TheLiteralist, 01-23-2005 00:43 AM
This message has been edited by TheLiteralist, 01-23-2005 00:47 AM

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TheLiteralist
Inactive Member


Message 22 of 98 (179823)
01-23-2005 1:02 AM
Reply to: Message 9 by NosyNed
01-16-2005 10:50 AM


Broken Genes
NosyNed,
Also we see that what are obviously broken genes are carried along for a pretty significant time. It is unlikely that these are both broken genes and of some other value (unless pure bulk is of value).
In my mind, the "broken" genes might simply be genetic modules that look very similar to other genetic modules but serve somewhat, or even altogether, different purposes. It is easy enough to make a few adjustments to a computer code module and have it serve a completely different function in the same or different program. (Why re-invent the wheel for each program, right?)
Also remember that the original designation of junk was based on the fact that it does not code for proteins.
So, apparently, there was a time when we didn't realize there was a purpose for non-protein-coding DNA; now we realize that there is.
Could it be that the "broken" genes serve legitimate purposes that are simply unknown at this time?
--TL
This message has been edited by TheLiteralist, 01-23-2005 01:02 AM

This message is a reply to:
 Message 9 by NosyNed, posted 01-16-2005 10:50 AM NosyNed has replied

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TheLiteralist
Inactive Member


Message 23 of 98 (179826)
01-23-2005 1:26 AM


random mutations v. purposed variation
I can conceive writing a computer program that copies itself and, each time it does, changes certain sections of the program on a random basis. Certain core areas of the program could be identified so that they could be prevented from being changed (or else the whole thing would quit or go haywire). Also, while randomness could be introduced into the program via a random generator module, test modules could be set up to ensure that the randomly generated code sequences met certain criteria (e.g., were valid code segments, weren't detrimental to the overall program, etc.) Or, the program could contain a sort of database of various code seqence snippets, and depending on results from the random generator module, various of these snippets could be copied into active modules. Thus, either way, the overall program sequence changes upon each copy (or it could be set up to change after X copies have been made, where X could be constant, variable, or randomly variable), yet the basic program remains the same AND the variants are a result of the original program AND each variant has the capability of making variants, too.
I don't think anybody on this thread has yet satisfactorily shown how we can distinguish between random mutations and on-purpose but randomly generated changes in the sequence due to some function or functions of the original sequence.
I would really like to know if and how such could be distinguished.
--TL

Replies to this message:
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TheLiteralist
Inactive Member


Message 25 of 98 (179841)
01-23-2005 2:14 AM
Reply to: Message 24 by crashfrog
01-23-2005 1:38 AM


Crashfrog,
There's simply no physical way in a thermodynamic universe to prevent mutation in any part of DNA. It can be reduced, and is, but it cannot be prevented completely as you suggest.
I have not said that mutations do not or cannot occur. I am asking how could random mutations be distinguished from on-purpose variations produced as a function of the code itself.
There's no test that operates on DNA except the expression of genetics in the morphology of individuals who are then selected for or against by the environment.
I certainly am not an expert on cellular biology. I believe that there are cell components that "correct" many "copying errors"...could that actually be a test similar to what I have stated in my programming analogy? (Perhaps it isn't...I don't know.)
If there were, we could detect the cellular machinery that did so; if you believe it exists its inbumbent on you to prove it, not us to prove you wrong.
Rather than making any assertions, I felt more like I was asking a question: "How can we distinguish between random mutations and on-purpose but randomly generated changes in the sequence due to some function or functions of the original sequence?" My analogies to computer programs are simply to give a better understanding of what I mean by the question. It is highly unlikely that I will ever find myself in a lab working with DNA. Yet, the question seems valid and easy enough to answer one way or the other for those, whose field is in an area dealing regularly with genetic operations and/or functions.

This message is a reply to:
 Message 24 by crashfrog, posted 01-23-2005 1:38 AM crashfrog has replied

Replies to this message:
 Message 30 by crashfrog, posted 01-23-2005 10:58 AM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 32 of 98 (179951)
01-23-2005 2:11 PM
Reply to: Message 28 by Ben!
01-23-2005 6:56 AM


Re: Broken Genes
Hi Ben!,
Or am I way off? I'm kind of out of the loop here.
I don't think you're way off, and I started the thread. I think that you have made a very honest observation.
--TL

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TheLiteralist
Inactive Member


Message 35 of 98 (182019)
01-31-2005 8:43 AM
Reply to: Message 30 by crashfrog
01-23-2005 10:58 AM


CrashFrog,
I do wish to clarify that I have not said that random mutations could not or do not occur. What I am proposing is that the DNA somehow codes for most variations (random changes in DNA structure). Such changes being, according to my beliefs, intelligently programmed would not affect certain key areas of the DNA. However, any number of non-DNA influences could cause random mutations. These non-DNA influenced changes (i.e., random mutations) would, in most cases, though, be deleterious.
In my programming analogy, the computer code commands random changes to occur in certain areas but not others. However, power spikes, faulty processors, etc. could cause the program to change anywhere, anyway, in any module..but this would not result in any planned for changes and would in most, if not all, circumstances cause the program to run inefficiently if at all.
Don't know if that clarifies what I'm trying to say or not.
--TL

This message is a reply to:
 Message 30 by crashfrog, posted 01-23-2005 10:58 AM crashfrog has replied

Replies to this message:
 Message 36 by crashfrog, posted 01-31-2005 11:16 AM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 37 of 98 (182111)
01-31-2005 4:52 PM
Reply to: Message 36 by crashfrog
01-31-2005 11:16 AM


By what mechanism?
I wouldn't really know the mechanisms involved. I get this whole idea from some reading about how the immune system works (in Michael Behe's book, Darwin's Black Box--his point was the irreducible complexity of the system, but that is not my point here). The t-cells or b-cells (or some kind of cells) can do some neat DNA shuffling just to try out different binding sites (if I remember how it works...forgive the vagueness). I don't know how the cells do that, but however they do, perhaps a similar mechanism would be what I am proposing (I think they even only use certain segments of DNA to arrive at the random sequence they will use for binding sites.) So I find myself wondering if cells in general are using something to make variation a normal mode of life, and we have incorrectly thought they are copying errors (i.e., sort of like the code demands a "copying error" to be made in certain places). In such a case I would expect the code to prevent (don't know how) certain areas of the genome from being affected.
Please understand that this is not something I've gotten off AIG or ICR, this is my own wondering. (So, if it turns out to be completely wrong, don't think this is mainstream (or any kind of stream) creationism). It's an idea born in a person with a high school level of understaning of biology, who's read Darwin's Black Box, and is just wondering about the random mutations thing. It is my understanding that most creationists accept the random mutations idea to some extent, but I am wondering how we can know that's what we are seeing.
Maybe you could explain how your model prevents macroevolution from occuring, because that would be the inevitable outcome of truly random mutations.
Yes. The code would not cause variation just anywhere or everywhere but would target only certain areas. Certain areas would be key for that particular kind (whatever God considers to be the kind--our own classification systems not necessarily being the same as His) and, therefore, would not be targetted by the code for variation. Random mutations could occur anywhere or everywhere, but I am proposing that truly random mutations (actual copying errors, radiation, etc.) would be useless or, most likely, harmful in some way and would quickly be selected out--perhaps ending with mutant organism itself.
Actually, to me, if all variants are due to truly random mutations, particularly in unicellular organisms, I find it difficult to believe that we could classify them (the bacteria and algae, etc) very easily...as they'd be changing significantly rather frequently I'd think. OTOH, if it is a pre-programmed, DNA controlled process, that could be the reason that the variants are numerous but the basic types of algae or bacteria, etc. stays the same.
If random mutation is still happening, then you have evolution. I don't understand how your model is fundamentally different than the evolutionary one. At best you have a sort of add-on theory that posits additional evolutionary change.
Well, in my "model" (if it can be called that), the DNA controlled variations are the main source of variations and, in general, are useful or useless and almost never harmful (and, therefore, may be selected). OTOH, truly random mutations would generally be useless or harmful (and, therefore, would generally be selected out quickly).
--TL
This message has been edited by TheLiteralist, 01-31-2005 17:00 AM

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Replies to this message:
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 Message 39 by Jazzns, posted 02-01-2005 11:47 AM TheLiteralist has replied
 Message 40 by Loudmouth, posted 02-01-2005 1:08 PM TheLiteralist has replied
 Message 49 by Ooook!, posted 02-02-2005 1:20 PM TheLiteralist has replied
 Message 52 by pink sasquatch, posted 02-02-2005 2:14 PM TheLiteralist has replied

  
TheLiteralist
Inactive Member


Message 41 of 98 (182467)
02-02-2005 2:15 AM
Reply to: Message 40 by Loudmouth
02-01-2005 1:08 PM


Foresight
Hi Loudmouth,
You being a biologist, I will consider much of what you say, much as I will give consideration to what Quetzal or Wounded King says--about this idea of mine at least. I am speaking mainly about the mechanics of it all, and not so much the interpretation as to whether it was intelligently designed or evolved or whatnot (though we'll certainly be sharing opinions on that as well, I'm sure--I mean, it IS EvC.)
I wish everyone to understand two things:
  1. I am NOT saying that this is the way DNA operates
  2. my "model" does NOT involve forsight of any sort (just as the immune system does not)
It is just an idea that I had, and I wouldn't be surprised if it turned out to work this or some similar way based on the idea that the genetic code is of intelligent design. However, if my idea is incorrect, that doesn't mean the code isn't of intelligent origin.
It'd be neat if I, a fast-food cook and college drop-out, had an idea that turned out to be the next great discovery that unlocks heretofore unknown genetic secrets, that sends shock waves through the scientific world...I'm not getting my hopes up about it, though.
It is obvious, to us creationists, that the Creator has created the code to allow for tremendous variation while maintaining, to an amazing degree (considering the changes that apparently occur at the genetic level), the stability of the various types of organisms.
--TL

This message is a reply to:
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TheLiteralist
Inactive Member


Message 42 of 98 (182469)
02-02-2005 2:23 AM
Reply to: Message 40 by Loudmouth
02-01-2005 1:08 PM


Mechanism?
Loudmouth,
I don't know much about DNA...looking at my "model" would you say that the mechanism that allows the immune system to be "sloppy on purpose" couldn't have a similar counterpart in the DNA replication of most any cell? Not necessarily exactly the same, but similar?
If there is, wouldn't you say that we could possibly be calling things random mutations, when in fact they are "on-purpose mistakes."
Once again, I re-iterate, I am not saying that my idea is true...I'd really like to know how plausible it is, though.
--TL
This message has been edited by TheLiteralist, 02-02-2005 02:24 AM

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Replies to this message:
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TheLiteralist
Inactive Member


Message 43 of 98 (182471)
02-02-2005 2:32 AM
Reply to: Message 39 by Jazzns
02-01-2005 11:47 AM


I Am Not Trying To Prove God Is Real
Jazzns,
I can understand you and others thinking this, but it isn't so. I believe God is real no matter how the DNA works. This is just an idea I had that was inspired by the fact that I believe God is real (i.e., the code is of intelligent design).
My "model" could be wrong or need to be modified or highly modified for all kinds of reasons...especially considering my low-level of biological knowledge (particularly of DNA). And my awareness of how little I know of biology and genetics is becoming clearer the more Wounded King and Quetzal type.
The reason I wanted to discuss this issue in this thread was because this thread is more focussed and because the other was getting near closing (and now has been closed).
Thanks for joining in.
--TL

This message is a reply to:
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TheLiteralist
Inactive Member


Message 50 of 98 (182587)
02-02-2005 1:50 PM
Reply to: Message 47 by JonF
02-02-2005 12:39 PM


Changing due to Need
Hi JonF,
I think I am having a time communicating my thought clearly, and I think that it would be easy to read what I've written and think that I am talking about variation being generated in response to need, almost like foresight.
However, this isn't what I'm proposing. I shall try to make my point even clearer in a later post.
Thanks,
--TL

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TheLiteralist
Inactive Member


Message 51 of 98 (182589)
02-02-2005 2:06 PM
Reply to: Message 48 by crashfrog
02-02-2005 1:17 PM


RANDOM and MUTATION
Hi CrashFrog,
I don't think he's proposing that; I think he's saying that because the mutation occured "on-purpose", that is a mechanism allowed or stimulated a mutation (but not the outcome of the mutation), the mutation was not "random".
I disagree because that's not why we call them random. We call them random because the outcome of the mutation event is not deterministic; in that sense there's no difference between what he proposes and what we term "random mutation."
You are almost right, I think. At the beginning I asked how could we tell the difference between what I am proposing and what is now called random mutations. The distinction would not be easy, and may not be possible at all.
You are slightly off in that, in my mind at least, what I am considering IS random in a way. The mechanism, whatever it may be, would control where the "sloppy on purpose" would occur, it might control the extent of the "sloppiness", and it might control when the "sloppiness" occurs (but all three things could be made to be random to some degree, in my mind at least, based on some computer programming I've done, tho I'm not sure that the DNA/programming analogy can be carried that far--it seems capable of such controlled randomness, tho, e.g., the immune system).
The main point is that WHERE and HOW the sloppiness occurs is somewhat controlled and would, therefore, be limited to what changes could takes place due to THIS mechanism.
My main problem is with the term MUTATION, which, I suppose could just mean change, but it has, for me at least (and I could be wrong), a connotation that it is a change that is either an unintended change caused by an error of the cell during replication or a change caused by some external factor such as radiation. I believe these things can and do happen, but that they would have mostly, if not only, deleterious effects since they would not be built into the function of the cell.
I appreciate your examination of the "model." Particularly your last post to which this post responds. I shouldn't be surprised if it is way off-base for one reason or another.
--TL
This message has been edited by TheLiteralist, 02-02-2005 14:07 AM

This message is a reply to:
 Message 48 by crashfrog, posted 02-02-2005 1:17 PM crashfrog has replied

Replies to this message:
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TheLiteralist
Inactive Member


Message 53 of 98 (182599)
02-02-2005 2:35 PM
Reply to: Message 49 by Ooook!
02-02-2005 1:20 PM


The All-Encompassing First Cell
Hi Oook,
I don't hold to the first-cell-with-all-the-info-for-everything model that Behe proposes. That is truly a bizarre proposal to me. I seem to recall reading his whole book thinking he was a creationists until I got to the end, and went "WHAT?!?"
But I think the idea of irreduceable complexity has much merit (though I'm aware evos don't). I also just enjoyed reading about the various biological processes he outlines in his book--such as a general overview of how the immune system can introduce "sloppyness on purpose" to produce random binding sites.
Reading of that process inspired this "model" of mine, but I don't see any connection between this model and irreducible complexity (maybe a slight connection to that one) or the first-cell-that-had-info-for-everything (especially not that one!)
Really, if the issue of intelligent design or evolution etc. could be laid to the side temporarily, I'd like someone to try to honestly see if the idea has any merit at all.
Is there a mechanism within the cell or DNA that is "intentionally" (for lack of a better word) producing random changes in certain areas of the DNA. I don't mean actual copying errors, where the cell meant to make a perfect copy and made an imperfect one, but intentional changes (which might look too much like legitimate copying errors to ever tell the difference). Would there even be a way to make this distinction???
It’s not fully understood how this hypermutation occurs but it has something to do with the recruitment of a defective DNA repair process to those areas. This seems to be the kind of mechanism you are proposing with your ‘intelligent programmer’ scenario, where mistakes are encouraged in certain areas and not others.
Yes, you are right, I think that is what I am trying to propose. In light of this comment, it may not be possible to even tell the difference between actuall copying errors and those induced on purpose for variation's sake. Plus I see here the word "mutations" being used even when the system is doing it on purpose, so to speak.
So really, CrashFrog is almost completely right in saying there is no difference...except that my "mechanism" (as I'm proposing it) would not affect just anywhere in the genome, but would likely not affect certain core areas of the genome.
I guess another inspiration for this idea is what appears to be the fact that bacteria and algae apparently variate tremendously. So much so, that I am becoming amazed that there is not some process to keep them stable enough that we can still classify them over the past century. If the randomization process is controlled to some extent by the DNA, that would make sense to me. The variants are only able to variate in certain ways and not in others. (I'm not saying I'm right...that's just the "model" I'm proposing).
Oh well, thanks for the response Oook!
--TL

This message is a reply to:
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Replies to this message:
 Message 56 by crashfrog, posted 02-02-2005 3:05 PM TheLiteralist has replied
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