I wondered, as you look over that large of a time-span, isn’t there some chance that you un-mutate back to the original gene? Is that what this means?
Not the original gene, but at any one site there’s a chance of getting back to the original base. If two sequences are randomized compared to each other, not every base will be different. If, for example we assume that every base is equally likely, then two randomized sequences will be identical at 1/4 of the positions. No matter how much time you allow, they will never get less than 25% similar, and that’s what “saturation” means.
Sure. And?
Um, yes there is a SMALL chance you can mutate back to the orginal sequence. It is a small chance, and usually neglected.
This is what I was trying to get at. You aren’t simply accumulating mutations until you’ve changed every single base. It’s like the difference between picking out a particular letter from the alphabet with or without replacement.
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Um, yes there is a SMALL chance you can mutate back to the orginal sequence. It is a small chance, and usually neglected.
It’s not neglected in phylogenetic analysis.
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.It was just neglected by @John_Harshman
I apparently misunderstood what you meant. I thought you were agreeing with his answer Jordan but indicating that the probability of back mutations was generally neglected. I see now that you were saying something different.
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Yes, because for a sequence of any reasonable length the probability of returning to an exact match through neutral evolution is small enough to ignore. But it’s also true, as @davecarlson implies, that phylogenetic analysis generally assumes a reversible model of evolution, so the probability of return to an exact match can be calculated.
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if so we cant estimate at all when 2 insects were split off from each other. so what this paper suppose to be?:
He said “this doesn’t mean”, so your “if so” makes an incorrect assumption. The paper used protein-coding sequences that are under selective constraint. I imagine that third position transitions are indeed completely saturated between any two species on the tree, but even silent third position transversions probably are not. At any rate they tried analyses with third positions excluded, and there was apparently no significant difference in outcome. Further, they did a likelihood analysis with a relaxed clock, which means that the rate of evolution was allowed to vary across the tree. Did you actually read that paper?
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Not at all. Just because X mutations doesn’t necessarily = Y split time, that doesn’t mean that mutations are uninformative about split times. Quite the contrary. Did you really think that I said what I said unaware that molecular clock analysis exist?
The abstract says:
Bayesian divergence times analysis, with reference to specific fossil constraints, places the origin of Holometabola in the Carboniferous (355 Ma)
Notice it doesn’t say “we counted the number of nucleotide differences, then divided it by the per-year mutation rate to obtain the split time”. These kinds of analyses are just a bit more complicated.
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no, i didnt read the paper. just give it as an example. im also not sure if i understood your explanation (im not a biologists and my english isnt so great) but if they checked for conserve protein sequence this may solve the problem. on the other hand, if the molecular clock method is so great then why to use fossils to calibrate it? i also noticed that they can use some DNA sequence like in this study:
so if we cant make a good insect phylogeny out of DNA sequence why to use it?
indeed more complicated. although why to use fossils if the molecular clock is accurate?
Did you read the paper? Oh wait, you already answered that:
Don’t you think you should probably read it before referencing it and asking questions about it?
And example of what? Since you didn’t read it, you can’t know what it’s an example of. But I’ll tell you: it’s an example of creationist quote-mining. If you can’t read the article and can’t understand my explanation, how can you possibly argue about this subject?
Because any measure needs to be calibrated?
Yes, and if the moon is made of cheese, why can’t we import Wensleydale from it?
When God is using evolution to create, suggesting that he is “twiddling” is a bit preposterous.
And the term “intervening” is equally off-point.
God is “Engaged”…in God-work!
It would be good to know what that means. Perhaps you can help?
Well, yes, of course God is engaged in God-work. But that could be said to be true even if there is no God and even if there is no such thing as God-work.
Your statement is a sophisticated-sounding way of saying nothing.
Please stop trolling me.
You wanted to call God’s use of Evolution as twiddling or intervening. It is neither.
It is ONE of the two ways God can create life that we know about. The other way is presumed to be SUPER-NATURAL, rather than natural.
That’s all we know, Johnny. Asking me the same question a million different ways is not going to help you.