Ok, first off I made a mistake in describing the situation with cytochrome C. CytC is a mitochondrial gene which means it is haploid, so there would not be two copies in each organism, but only 1. It is also inherited primarily through the maternal line, so there is no recombination with the male counterpart. So in reality we would expect only 1 haplotype to exist in the original ark pair - although I could be open to the idea that multiple sequences existed in the same organism.
Then how could it possibly be a species identifier?
This explains, in part, why the study Genomicus cited showed increasing genetic diversity while other reports suggest that the population has not recovered from their genetic bottleneck. Elephant seals are highly polygamous, meaning that a single dominant male will fertilize between 30 and 100 females. This greatly reduces the effective population which in a population with only a few dominant males getting all the action, the effective population could be as low as 1/10th the actual population. In addition, the dominant male would be breeding with his own daughters and granddaughters further increasing homozygosity. Mitochondrial DNA does not have these problems. So it should be clear why the discrepancy between the two systems.
One saying no increased genetic diversity, the other saying yes increased genetic diversity. Fine, you've explained the discrepancy but not solved the problem of whether there is increased genetic diversity or not. Seems to me that the mitochondrial DNA measure in fact says nothing about the true situation, which in reality is that increasing homozygosity brought about by the mating patterns, which would be severe enough even if the seals mated for life but of course exacerbated by the dominant male pattern. Obviously the mitochrondrial DNA method is useless as a measure of genetic diversity so why is it used at all?
But I digress...
Maybe, but that discrepancy is of paramount importance in this discussion, and what you've illuminated is that it makes zero sense to use mitochondrial DNA as an indicator of genetic diversity. It could say there's a big increase in genetic diversity while the creature goes extinct from all that increasing homozygosity.
So back to cytC.
So each separate breed of dog has its own unique cytC sequence? You can identify, say, a spaniel from a wolfhound from a poodle by their own unique sequence?
Yes and No. Theoretically you should be able to trace a lineage through the maternal line, so in that way, yes, each breed or more precisely, each
breeding population should have its own identifying sequence.
Huh? Why would its being passed on through the maternal line produce a different sequence/species identifier in the offspring?
However, the amount of differentiation between sequences is probably not sufficient to identify a specific breed.
How are you getting any "differentiation between sequences" at all in the first place?
The other complication is that contrary to what you are suggesting, the main way that new breeding lines are developed is by the introgression of desirable traits into a preferred genetic background and then selecting for those desirable traits (think 'gene flow'). Rather than 'muddying the waters', gene flow provides variation for which further evolution can operate. How this complicates the cytC situation with dogs, or other breeding programs, is that if a trait was introduced from a male parent, there would be no mitochondrial record of that introgression. So mtDNA (mitochondrial DNA) has its uses in breeding programs, but it is not used for ID.
That entire paragraph is absolute gobbledygook to me. I have NO idea what this means: "the main way that new breeding lines are developed is by the introgression of desirable traits into a preferred genetic background and then selecting for those desirable traits (think 'gene flow')." Absolutely zip. Not only does it not tell me anything about why I'm wrong about breeding practices, it doesn't tell me anything at all about breeding methods, period. What is an "introgression?" what is a "preferred genetic background?" What I've described of breeding practices is so well known, not only is this statement undecipherable, but insofar as it aims to contradict what is well known it's ridiculous.
Or a Persian cat from Siamese? Or from a lion, or a lion from a tiger?
A grizzly from a polar bear?
Persian from Siamese - Probably not. Same deal as with dogs above - although I don't think cat breeding history is as complicated as dogs.
House cat from a lion - Yes
Lion from a tiger - Yes
Grizzly from a polar bear -Yes
Rat from a mouse - Yes
But you've said absolutely nothing about how these different species get or don't get a particular species identifier. Ordinary reproduction should pass on the same identifier indefinitely, so in related species how do they get different identifiers?
Below is an alignment of a rat sequence and a mouse sequence. Where there are not vertical bars between the sequences indicates a difference in sequences - ie. a mutation.
1) I can't read it because it blinds me, and 2) I have no idea what I'd be looking for if I could read it, why the supposed mutations matter, how the rat and the mouse got different sequences and so on.
IIRC, the sequences had 95% or 96% identity. So if I had a sequence and wasn't sure what it was, I could compare it to a database and I might find that it matched 99% with a mouse sequence and 95% with a rat sequence and I could conclude the sequence was from a mouse.
If I did the same thing with a dog sequence, I would probably return dozens of sequences from many different breeds that had 99% identity, so while they may be different and even unique, it would not be conclusive enough to assign the sequence to a specific breed. However, it may be different enough from a wolf and certainly would be from a coyote or a fox.
I'm sure this makes sense to you, and you think you are explaining something to me, but if anything it's making the whole issue more mystifying.
*******Side topic alert*********
You can eliminate drosophila from the list because God didn't command Noah to save insects or bacteria, or even plants for that matter, although I'm willing to think about plants.
This is what puzzles me about literalists.
quote:
Gen 7:21 - 23
And all flesh died that moved upon the earth, both of fowl, and of cattle, and of beast, and of every creeping thing that creepeth upon the earth, and every man: All in whose nostrils was the breath of life, of all that was in the dry land, died. And every living substance was destroyed which was upon the face of the ground, both man, and cattle, and the creeping things, and the fowl of the heaven; and they were destroyed from the earth: and Noah only remained alive, and they that were with him in the ark.
*Literally*
"every living substance was destroyed" and
"all that was in the dry land, died." which includes
"every creeping thing that creepeth on the earth,". I guess I understand plants not being on the list, but insects? It is abundantly clear that ALL animal life was completely wiped off the face of the earth, yet literalists want to interpret this in some other manner than a simple, straightforward, literal reading.
Huh? We all figure insects died too. We also figure they managed to survive in much reduced numbers without Noah's help, as hitchhikers on the ark or some other way, and that there were plenty of seeds for plants on the ark, as well as some that survived in the land to sprout after the Flood. But that is not the same thing as Noah's being specifically required to save them. He also was not commanded to save sea creatures, so although obviously huge numbers of them died, some also survived the Flood. So for whatever reason the creeping things are not identified with insects, and I'm just going by what most theologians say about them. I don't get why you have a problem with any of this.
The more I think about this the less sense it makes.
The problem is that rather then looking at the evidence at determining what it tells you, you are trying to get it to fit the narrative you have created. I can understand why it would not make much sense.
That is a completely gratuitous unfair accusation. I'm doing my best to understand your completely garbled presentation of these things.
1) These alleles are species identifiers, you say, so how is it that two individuals of the same Kind/Species would have four different species-identification alleles among them?
They wouldn't. I was trying to fit these observations into an imaginary scenario (and by imaginary here I simply mean that rather than being able to go somewhere and learn about this hypothesis of yours, I have to imagine what it means. Whether it is imaginary in the sense of being not real is what we are discussing).
Maybe you should just try explaining what you know instead of making up straw men.
2) When that pair mates, say they are dogs, they aren't going to have four new species or even one new species, they are going to have a litter of puppies. Which should all have the same cytC identifier since they are all of the same Kind/Species, shouldn't they?
3) After they grow in numbers to a sizeable population then they might split off into subpopulations and eventually become new subspecies of dogs. But they'd all still have the cytC identifier for Dogs, wouldn't they?
What are you saying? That when a new subspecies emerges, at some point it gets a new cytC identifier? What would bring that about? At what point would you expect it to emerge in the process of its evolution?
Just to be clear, cytC does not
determine the species, it
identifies it. Meaning there is nothing about the sequence that gives an organism its unique phenotype. cytC sequence changes occur independently of what is happening in the nuclear genome.
It never occurred to me to think it would determine the species. What a strange idea. Also the fact that these sequences change independently makes it hard to link them at all to the species. How they become species identifiers is still unexplained.
Mutations in the cytC gene accumulate in step-wise fashion.
No idea what that means. Sounds rather programmed for an accidental or random replication mistake.
Within a breeding population, there will be some variations in sequence; not all members will have identical sequences. Perhaps a sub-population splits off from the main population. This sub-population will continue to accumulate changes, but these accumulated changes will be different from the parent population. Over time the sequences of the two populations will be recognizably different. During this same time, changes are also occurring in the nuclear genome. When these changes in nuclear genes are sufficient to prevent (or minimize) interbreeding with the parent population, the changes in cytC have diverged sufficiently to be used to be identified with that new species or subspecies.
Another thing to clarify, there is nothing specific about a cytC sequence that allows one to identify the species, it is comparison to known samples from a database that provides identity. If no representatives from a species has ever been sequenced, a search may present no close matches. It this case, you may be able to say that it is closely related to some other species, but not a close enough match to identify it as a specific species.
???
This can be a powerful tool in understanding the history of a species and what has driven its evolution. If a pattern and pace of nucleotide changes have occurred in the cytC gene since a population diverged, one would expect similar changes to have occurred in similar nuclear regions. If they haven't, if the pattern and pace is significantly different that expectation, it is an indication of one of the evolutionary forces at work. Often a gene tree will be developed based on a region such as cytC (the standard now is 4 or more independent regions) and other traits will be overlaid on the tree to study how they have changed or how they vary in different species.
I know you probably think this is completely irrelevant to your argument, but its is relevant. The patterns we observe require an explanation. Here's where that comes in...
All I can think is that if it is a species-identifier then it is a Dog identifier, not a dog-breed identifier, in other words it is an identifier of the Biblical Kind or Species. If that's the case then it would make a wonderful way of defining what a Kind is.
Yes, that would be the expectation, wouldn't it. Based on what I have said about the system in this post (hopefully it is a bit clearer) how would you predict that one could distinguish between "kinds" using this method? Saying that the sequence of a dog should be more similar to another member of the dog kind than it would be to a cat kind is not enough, since that is also what the ToE would predict. How would you predict that there would be disparity between the kinds? How would you recognize different kinds?
I think if nothing else, this should make it clear that mutations do occur and accumulate. I know you have allowed for "some kind of mutation" meaning... I don't know what. Yes, the mutations in cytC are essentially neutral, which is maybe the "some kind" that you allow for. But, the bigger point is that we see this same pattern at play in nuclear coding genes. But we'll have to cover that later, once you understand the point about cytC and how it is used.
Now MAYBE if I read all this a few dozen times some kind of light would be shed on it, but as it is I'm afraid I'm no less in the dark than I was before.
Edited by Faith, : No reason given.
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