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Author Topic:   Introduction to Genetics
Faith 
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Message 56 of 236 (719178)
02-12-2014 12:34 AM


The Specific Genetics of a Specific Species
I just skimmed this thread starting with my original questions. A lot of them did get answered although the thread took a much too technical turn for me.
The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another. Like they say there is only about 5% difference between the human genome and the chimp genome. That 5% of the human genome then must contain the coding for what is specifically human and not ape, and same with the ape genome. But is that particular 5% even recognizable, is it clear in the genome where it is located and what it codes for? In other words I'd really like to know the specifics about that part of every genome for every creature that differentiates it from all the others. What makes a cat genome a cat genome, a dog genome a dog genome etc?
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 61 of 236 (719293)
02-12-2014 8:33 PM
Reply to: Message 59 by Taq
02-12-2014 5:45 PM


Re: The Specific Genetics of a Specific Species
Thank you for the answer. I want to spend some time on it, checking the links and so on, but I have a question right off:
The question that brought me back to this thread is really a wish to know what differentiates the genome of one species from another.
The answer is the order of nucleotides on the DNA strands.
Irrespective of genes or what? How long a strand are you talking about?
Like they say there is only about 5% difference between the human genome and the chimp genome.
That means that when you compare 2 homologous strands of DNA there will be the same base 19 out of 20 times when comparing the two genomes.
Again, my question is what is a "strand" of DNA, how long a strand, in relation to a gene for instance, or a chromosome, etc.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 68 of 236 (719343)
02-13-2014 1:18 PM
Reply to: Message 62 by Taq
02-12-2014 11:51 PM


Re: The Specific Genetics of a Specific Species
So a strand is basically a chromosome?
So it's just the sequence of nucleotides irrespective of genes, and 19 out of 20 in the sequence are identical between the two species in question? Chimps and humans.
So that means for the two species being compared the same genes are in that sequence in the same order with the same stop codes and all that? The only difference is the one out of twenty nucleotides that is different along the whole strand and those occur in the genes of course but for some reason the genes themselves aren't relevant?
But there must be different genes in the different species, no? ABE: Of course the difference in nucleotides would make for different genes, but I'm thinking of different genes as entirely different segments of DNA, entirely different locations on the strand. From what you are saying it's all the same as far as the location and order of the genes go, only the one in twenty nucleotides along the entire strand is the defining thing. /ABE
Is there a clearcut pattern to the location of the species-identifying nucleotides in that chain of 20? I mean does it occur at predictable intervals or just show up willy-nilly so you have to sort out the entire strand to recognize them? I'm not sure this question makes sense. I guess I'm trying to get an idea of how regular or predictable or how much of a recognizable pattern is involved.
If these questions don't make sense that's OK.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 73 of 236 (719383)
02-13-2014 8:13 PM
Reply to: Message 69 by AZPaul3
02-13-2014 4:08 PM


Re: The Specific Genetics of a Specific Species
No. No predictable pattern. There are long stretched of the genome where every letter is different between chimp and human and there are even longer stretches of code where the sequences are identical. Over the entirety of the 2 genomes there is the 5% difference.
I'll ignore your remark about the bonobo and I'm glad Nosy called you on it. But thanks for this answer, it's informative.
Of course I'd really like to know WHICH stretches have different letters and which the identical sequences because I'm very much interested in which traits are involved.
And again I'm still interested in where the genes fit into this. I mean they ARE clearly demarcated segments of the DNA with their start/stop codes, right? And they DO determine very specific traits in the organism, right? (Referring to discussion with Devils Advocate where he seemed to think mutation could actually change what a gene DOES, whereas I was arguing that the gene always does whatever it does but that alleles change the specifics of how it does it. Like if a gene makes eye color its various alleles are only going to determine WHAT eye color and not change that gene into one that makes eyelashes or bellybuttons. Right?
Edited by Faith, : change stop to start/stop

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 75 of 236 (719395)
02-13-2014 9:47 PM
Reply to: Message 72 by Taq
02-13-2014 5:43 PM


Re: The Specific Genetics of a Specific Species
There are also insertions and deletions, which we call indels (a mash up of the two words). This produces gaps when we try to align the two DNA sequences. You can see the indels in this alignment:
So are you saying that the indels are the same in the same species but produce gaps in the genomes between the two species?
Indels are mutations, though, aren't they? (Meaning, I guess, that there would be gaps between the DNA of two individuals of the same species too, wouldn't there?)
ABE: OR, are you saying that the indels simply reflect differences in the presence or absence of certain sequences between the two species; that is, that the indel is defined BY its difference from the other species? /ABE
The next type of difference is recombination where DNA is moved from one position in the genome to another, or even duplicated.
When you say "moved" or "duplicated" you are implying evolution, but I have to translate that into purely descriptive terms, which comes down to saying that the DNA in question occurs in different positions in the genome of the different species? Or is duplicate in the one but not the other? And I assume you mean as a regular feature of the genome of each?
When we compare genomes we determine if two genes are orthologs, homologs, or paralogs. An ortholog is a homologous gene found at the same spot in both genomes. A homolog is the same gene, but not necessarily in the same spot in each genome. A paralog is a duplicate gene.
So, trying to be sure I get this clear in my head, these different situations of the genes are considered to be identifiers of the species, that is they are predictable regular occurrences in the species genome for all individuals? If so, such differences ought then to be important identifiers of a species. When you say "the same gene" I assume you mean it's a gene that makes the same trait in the organism in both species, say fingernails or eyelashes or whatever. What exactly does a duplicate gene do in the organism?
It's really amazing to think that a sequence of protein-making chemicals can build a trait at all of course.
But there must be different genes in the different species, no? ABE: Of course the difference in nucleotides would make for different genes, but I'm thinking of different genes as entirely different segments of DNA, entirely different locations on the strand. From what you are saying it's all the same as far as the location and order of the genes go, only the one in twenty nucleotides along the entire strand is the defining thing. /ABE
I can't find the info very readily, but if memory serves, there are only a handful of genes in chimps and humans that do not have homologs in the other species. If I were to ball park it, I think there are around 20 genes in chimps that do not have homologs in humans compared to about 30,000 genes overall. If I run across the info again I will give you an update.
And again, homologs being genes that determine the same trait in the organism and occur in the same location on the DNA strand,
30,000 genes in the whole genome? That sounds small somehow. Aren't there thousands on one chromosome?
And again of course I'd be particularly interested in those genes that DON'T have homologs in the other species.
Is there a clearcut pattern to the location of the species-identifying nucleotides in that chain of 20?
There are many patterns, enough to fill this entire paper:
Nature - Not Found
. . . and then some.
Everything to this point was something I could deal with. Now it gets into mystowacko evo territory:
From the abstract:
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor,.
Of course an article that assumes evolution as this one does is alienating to a creationist. I have to try to translate the references to supposed evolutionary changes between the two species into purely descriptive terms. And if I may say so, that's what such a paper should do to begin with, to be genuinely scientific: stick to a simple description of the phenomena and avoid that tendentious interpretive baggage that assumes evolutionary transformation, or confine it to a part of the article for that interpretive purpose.
It would then read something like this:
"...we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor between humans and chimpanzees."
And I might as well do the same for the rest of it:
constituting approximately thirty-five million single-nucleotide changes [differences], five million [different] insertion/deletion events [locations?], and various chromosomal rearrangements [differences in arrangement].
I wasn't sure how to describe the differences between the indels, except that if there was never any evolution between chimps and humans we can't speak of "events" so the comparison has to be merely between different locations in the genome. Again, I think it's VERY unscientific to assume evolution and use such tendentious language in a paper like this, not just because I'm a creationist but because it's unscientific. But that's how we find it everywhere, also in presentations for the public. It's not right. Even if evolution were true it's not right. First you have to simply identify the comparisons you are making and then you can interpret it in terms of evolution, but even then you should be aware that it IS an interpretation, there is nothing in the facts themselves that demands that interpretation.
The rest of it may be too hard to translate:
We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
To me this is all pure fiction. I can't even really glean a descriptive fact from it though there must be some such facts buried in there somewhere. Is it saying that humans and chimps have the SAME fixed neutral and slightly deleterious alleles for the same genes or what? Can YOU translate this paragraph into simple descriptive terms for me?
Well, it's just the usual presumptuous assumption of evolution. And of course since I'm convinced it's all an illusion, all this conjuring of supposed evolutionary differences is someday going to collapse in a great scary muddle leaving you all perplexed to the max. But oh well.
Anyway, at least you yourself have been mostly helpfully descriptive, thanks, but now you are going to stop being helpfully descriptive. You go on:
Overall, there are fewer differences in gene and functional non-coding regions. However, that's a bit circular since function in non-coding regions is determined by divergence rates.
Which of course implies evolution again. Fewer differences between what and what? I think the evo baggage of that abstract has thrown me. And what "function" is there in "non-coding" regions which I guess refers to pseudogenes or junk DNA that apparently retains some function or what?
Perhaps it is better to say that some regions are diverging at a slower rate than others.
Please don't use terms like "diverging" which implies evolution and requires me to try to figure out what actual simple fact of comparison is being referred to.
The conserved parts of the genome are spread out all over. Suffice it to say that there are a lot of papers covering signals of selection in the human and chimp genome, so I can't really summarize it all here.
I can't make sense out of "signals of selection" I need simple descriptive facts, as in "this differs from that" and so on. Thanks.
Well, I was doing OK through the homologs and all that, but now I'm lost.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : add the ABE about indels

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 78 of 236 (719455)
02-14-2014 6:06 AM
Reply to: Message 77 by dwise1
02-14-2014 1:31 AM


Re: Speciation
In the topic, Bill Nye vs. Ken Ham, we had gotten to the point of needing to determine how long a speciation event would take. I'm talking post-coital barriers, to the point where genetic differences would prevent interbreeding between the new species and the parent species.
How long, in number of generations, would we expect that to take? Is it due to specific mutations, or just a general increase in difference between the genomes?
It depends on where you start, how much genetic variability is left in the genome of the particular creature at that particular stage in its (micro) evolution along a particular line of variation, and how many individuals each new population starts with -- the fewer the faster you're going to get significant change both phenotypically and genetically.
I think speciation would be due at least in this scenario to a general increase in difference between the genomes, since I don't think mutation contributes anything whatever of benefit.
ABE: I see from Tangle's reply that I'm going to have to state every time that although I use the term "speciation" because it does describe something that actually occurs, I do NOT regard it as macroevolution but merely a subspecies of a species that has become unable to interbreed with others of that species, probably mostly due to changes in the genome. AND I would expect it to have LESS genetic variability than the earlier populations, which certainly doesn't justify the optimism of calling it a new "species" anyway. /ABE
Edited by Faith, : No reason given.
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 90 of 236 (719488)
02-14-2014 1:09 PM
Reply to: Message 79 by Tangle
02-14-2014 8:31 AM


Re: Speciation
No, I guess I need to say it every time it comes up, I do not regard speciation as macroevolution, it is an event that does occur though so I keep the name for it, but it is merely a population, a race, of a particular species that has lost its ability to interbreed with others of that species, probably most often due to changes in the genome. And the kicker is that it should have less, little or no ability to vary further, making it an odd misnomer within the ToE anyway.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 91 of 236 (719491)
02-14-2014 1:41 PM
Reply to: Message 80 by herebedragons
02-14-2014 9:24 AM


Re: Basics of mutations
There is WAY too much going on in this thread now. I'm still back trying to deal with Taq's earlier post, and though it seems you are trying to help with that you've mostly given me more problems to sort out.
I don't think we've got to a point where mutations ought to be the topic. I'm still trying to understand some of the comparisons Taq's post described between humans and chimps, just descriptions of facts in the genome.
Thanks to you and N.Ned at least for agreeing that it is not necessary to use evolutionist language in describing comparisons between species.
=============
ABE: Aaaaagh! Could we please have a moratorium on bringing up anything new on this thread? I'm struggling through posts way back there already, there are unexpected miscommunications as usual to complicate things, and I'm afraid I've already lost track of some issues I'd really like to understand better.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 92 of 236 (719492)
02-14-2014 2:16 PM
Reply to: Message 84 by Taq
02-14-2014 11:06 AM


Genetic variability on the Ark
(dwise)
Can it be said that a single pair of organisms possess a vast amount of genetic variability? Or any individual? Or isn't it that you need to have a population in order to compare the individual genomes of its members to determine how much those individual genomes vary with each other?
(Taq) Depends on the species and the paif of organisms. A pair of human, identical twins will have nearly identical genomes and near zero variability. A pair of random humans with no recent common ancestor will have much more variability between them. A random set of chimps will have even more variability between them. A random pair of cheetahs will have very little variability because they went through a recent genetic bottleneck.
Yes, thank you!.
For the Ark scenario, it can not be said that just 2 individuals can have the same genetic variability as a population. For example, some of the MHC genes have thousands of alleles in the human population. Each person only carries 2 alleles. A pair would only have 4 alleles between them.
Not the same variability as a population, no, and I am aware that an explanation is needed for the many alleles in the population for some genes (ABE: though I have no idea what MHC refers to), which could not have existed on the ark.
But on the ark there could have been four different alleles for each pair or couple for many more genes than would have that many alleles today, though I'd have to suppose some attrition since the Fall, AND I'm sure this won't sit well, but if what is now junk DNA or pseudogenes was functioning DNA in the people and creatures on the ark, which I think very likely, then there would have been as much as 95% more genetic variability through that source than exists today.
The only way around that is if those ark pairs were extreme polyploids, carrying thousands of copies of the genome each.
Not likely of course, so some other explanation is needed. Perhaps some form of mutation then.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 94 of 236 (719496)
02-14-2014 2:35 PM
Reply to: Message 93 by herebedragons
02-14-2014 2:31 PM


Re: Basics of mutations
No no no no no no no. Not mutations yet, let's just stick to what had already been brought up. And I'm sorry you didn't mean what I thought you meant about evolutionist language.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 96 of 236 (719502)
02-14-2014 3:28 PM
Reply to: Message 95 by RAZD
02-14-2014 2:49 PM


This thread should be about facts not interpretaions
Insisting on definitions does not belong on this thread. I'm a creationist and I have a different way of understanding the data than you do and your attempt to force it down my throat is unwelcome, especially on this thread.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 100 of 236 (719513)
02-14-2014 4:16 PM
Reply to: Message 98 by AZPaul3
02-14-2014 3:45 PM


Re: This thread should be about facts not interpretaions
I did remove the militant "Get off this thread" at least.
"Macroevolution" in relation to speciation is an artificial definitional ploy. The actual FACT of speciation is merely that a subspecies has acquired the inability to interbreed with others of that species. That's the simple fact and to insist on it is NOT to give an alternative (creationist) interpretation, but merely to insist on correct factual description.
I can't do the same with "speciation" because in that case it does describe something that actually happens so it would cause confusion to insist on the falseness of the definition, so I'm stuck with simply having to write out my view of it every time if I want to avoid the usual objections.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 104 of 236 (719518)
02-14-2014 4:47 PM
Reply to: Message 99 by RAZD
02-14-2014 3:59 PM


Re: This thread should be about facts not interpretaions
Curiously I am not insisting on definitions, just pointing out that when you use a word that is commonly understood to mean something else then you are not communicating clearly, and then you end up complaining later about how people don't understand your points.
Speciation is not macroevolution and it isn't necessary to use that term. It's also not speciation either but I can't see a way to change that term, so I'll just have to keep writing out my view of it.
So you now concede that both microevolution and speciation occur as part of the natural world post flood ... wonderful.
There is no concession involved; I've viewed it this way for years and I'm sure I must have said so years ago already even here.
The theory of evolution can be stated as the theory that microevolution and speciation are sufficient to explain the diversity of life as we know it.
You are well on your way -- here and on some of the other threads -- to demonstrating that you believe this is sufficient to explain the diversity of life since the flood.
Except that there is nothing new about my view of these things, and speciation is not speciation, and there are many subspecies that belong to that diversity that aren't the product of speciation.
As I said, you are being forced by reality to either acknowledge basic evolution or deny reality.
Sorry but you completely misunderstand my point of view.
I will apologize for telling you to get off the thread though. Just the usual temper flare I have to curb.
Message 94: ... Not mutations yet, let's just stick to what had already been brought up. ...
ANY change to DNA is a mutation, so you are well into mutations already. Baulking at words that describe what you have been describing is not argument but denial.
It is important that I use words that say what I mean and avoid sounding like I agree with evolutionist concepts I don't agree with. It is not an easy task to negotiate these differences between the models, ABE: especially in the teeth of the militant insistence on evolutionist terms as factual, which they are not /ABE. In the case of mutations, I do NOT agree that alleles are the product of mutations, they are built in variants of genes, built in from the Creation. Mutations hardly ever, and probably in actuality never, create viable alleles that perform the functions of normal alleles. Mutations may manage not to destroy their function, that is, they may be "neutral," or they may be many degrees of deleterious to the gene, or they might even bring about the death of a gene, which I think is how some of the junk DNA was formed (though I think most of it reflects the mass death of the Flood bottleneck), and the mere assumption that any allele was the product of mutation should be avoided on this thread. If there is some reason to assert it then it should be asserted and not assumed. But most of the time I don't see that there would be any reason to assert it at all. The idea that there is EVIDENCE that alleles are the product of mutation is false, but if someone wants to defend that then it should come up when we finally get to mutations.
Although it is going to be necessary to discuss mutations on this thread eventually, it ought to be possible to describe allelic variants simply factually or descriptively without involving the interpretation that they were created by mutations.
Just look at your aversion to the word "divergence" ... most amusing the length you went to.
I'm not amused. "Divergence" is an evolution-specific word. Simple factual comparisons of differences between the genomes of different species are all that's needed on this thread.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 105 of 236 (719519)
02-14-2014 5:05 PM
Reply to: Message 101 by herebedragons
02-14-2014 4:23 PM


Factual versus interpretive tendentious terminology
I know. Let's talk about human / chimp relatedness but don't bring up mutations and don't use evolutionary language. Talk about stacking the deck.
I would like to point out again, and insist on it, and hope you will give it some careful thought, that all I'm asking for is simple straightforward factual descriptive terminology. That is NOT stacking the deck from my side at all, it is a completely neutral way of discussing the material at hand.
What IS stacking the deck is the evolutionists' use of INTERPRETIVE terminology. Please think about it: "Macroevolution" is an interpretation, it is not a simple factual description of what has actually occurred. "Speciation" is an interpretation, it is not a simple factual description of the fact that a subspecies has simply become unable to interbreed with its parent species. "Divergence" is an interpretation, not a simple factual description of the differences between chimp and human DNA. "Mutation" as used in many contexts is also an interpretation, an assumption, when it implies that it produced all the known functioning alleles.
All these terms are tendentious and interpretive, and all I'm asking for is neutral descriptive factual terms.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 110 of 236 (719536)
02-14-2014 9:28 PM
Reply to: Message 108 by Tangle
02-14-2014 7:02 PM


Paradigm clash
No, I guess I need to say it every time it comes up, I do not regard speciation as macroevolution. it is an event that does occur though so I keep the name for it
That's convenient, so long as you can have a personal definition of a term you're safe.
Nobody here seems to understand the nature of this debate. It really is a paradigm clash. Paradigm clashes involve different views of the facts. That involves different definitions, certainly in a case where the prevailing paradigm has stacked the deck with interpretive views of its own, which is the case with the ToE. If the ToE had simply honestly stuck to simple descriptive factual definitions of words the clash would not be as severe as it is. While paradigm clashes usually do involve some degree of hostility between the views, it's not scientific to try to define your opponents out of the argument, let alone force your terminology on them, and heap ridicule on them and all the rest of it.
It doesn't change anything about the facts though does it? If the creation of a new species is not a macroevolution event wtf is it?
As I said, it's not the creation of a new species; it's a subspecies that simply happened to develop inability to interbreed with the rest of its species. There is no other difference. The only reason it is called "macroevolution" is because of the definition of a species as incapable of breeding with others. That may or may not be the best definition in general, but when one knows that the speciation event is merely the loss of that ability in a known subspecies, the definition is decidedly artificial.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 108 by Tangle, posted 02-14-2014 7:02 PM Tangle has not replied

Replies to this message:
 Message 112 by Coyote, posted 02-14-2014 9:54 PM Faith has replied

  
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