It’s a claim without any substance. What does explain the data mean? What data specifically?
Bill isn’t a troll. He’s sincere in his creationism, though coy about it. He just doesn’t understand anything he’s talking about, but that doesn’t stop him from having strong convictions.
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What parts of the genome are not constrained? How do we know this without knowing the starting sequences. We know there is less constraint in mutations that do not generate amino acid substitutions but this is a very small part of the genome. The other sequences that maybe neutral are introns. Are introns junk? Not if their length is critical to gene expression timing during embryo development.
The point I am making is the logic being used implies assumptions that are not necessarily factual.
I would advise Bill to read Larry Moran’s book, but on several levels it wouldn’t help. He wouldn’t read it, he wouldn’t understand it if he did, and if he understood it he would manage to discount it anyway.
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I am sincere in my creationism 
John, you are advocating a model that gene, chromosome and genome evidence does not support. The model only stands because of methodological naturalism.
Restricting analysis to methodological naturalism makes your bald assertion “the only explanation for the nested hierarchy is common descent” fit the data.
Does Larry’s analysis depend on the inference of universal common descent?
Are you claiming that Bill’s ubiquitous sealioning isn’t a form of trolling?
One can be sincere in one’s beliefs, but still dishonest in the way one goes about defending them. And I would say “coy” is a gross understatement. 
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Come on. You have been around long enough to know which parts of the genome I am talking about. It’s the parts that Larry Moran refers to as “junk.” The parts that you say are not junk. The parts that are the subject of the discussion between you and I. Those parts. Is that enough specificity for you to comprehend which parts I am referring to?
I appreciate you are trying to make a point rather than answering my very straightforward question, but you may have noticed I am not interested in a diversion. I just want to know the answer to my very basic question, which was in response to the very first thing you said to me on this thread. I just want detail on that first assertion. If you didn’t even know what you yourself were referring to in that first assertion, I don’t know how you expect to have an intelligent conversation.
Just answer my question.
No. Does it concern you at all that everyone thinks it’s useless to try to discuss anything with you?
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It is not.
No, it is not. Though it is surprising why you, of all people, would consider it a problem if it were.
That’s not what you said was vague. You said “Explaining the pattern of the differences is a vague claim”, not “Explaining the data is a vague claim”.
But, to answer your question, explaining the data means contextualizing the data with a model whence accurate predictions of related future data can be rendered at a relatively low conceptual/computational cost.
The data, in this case, refers to the distribution of differences between pairs of genomes.
The ones that mutate freely and quickly without seriously impacting the lineage’s survival prospects. That is, to my understanding, a greater set than the set of genome parts that can be knocked out completely and still leave a genome that produces a viable organism, mind you.
By measuring mutation rates of various genomic regions, measuring how altering or knocking out a given region of a reproductive cell’s genome alters (or fails to, as it were) the thence growing organism’s traits. You know… experimenting. Like what we do in science.
Oh, also, we can know the starting sequences, if we have a sufficiently complete picture of the nested hierarchy.
I am no geneticist, so I cannot adequately address the specific questions you raised above the quoted passage, but as you say, those details are not your point. Your point, you say, is about the necessary factual-ness of assumptions underlying some logic. In my opinion, this betrays a misunderstanding of the fundamental character of the discourse.
Science isn’t maths. We are not in the business of proving things, necessary factual-ness is at most a secondary concern. The primary concern is how well or poorly predictions deduced from any given model – with its assumptions, for better or for worse – match with experimental observations. If all of a model’s premises were proven beyond any reasonable doubt to be false tomorrow (what ever that could possibly look like, given science’s inability to differentiate, in the strictest sense, between “truth” and “falsehood”), while I’m sure it would have the experts rush to come up with something new without such flaws, it would do precious little to undo the demonstrable usefulness the model had thus far, and it will remain useful and in use, likely even well past the point of the new alternative’s maturing, should such occur one day.
Please, name one piece of gene, chromosome, or genome evidence that is not consistent with the model, and explain how they are in conflict.
That contradicts what you said immediately prior. Something that is not supported by the evidence cannot stand because of methodological naturalism. Methodological naturalism demands evidentiary support for a model to not get discarded. You can have one or the other, but not both.
No. The experimental evidence has no care for what restrictions we place on our analysis. If you can produce a second mechanism by which nested hierarchies of genetic changes may occur, by all means, let’s hear it, see what experimental outcomes it implies, and test for them. That common descent is at least a mechanism is well beyond doubt at this point. That it is the only one is an admittedly “bald” claim, but it is the simplest, most parsimonious one until there is any demonstration that something else is possible.
Well, I’m glad we at last agree it’s an inference, not an assumption, as you used to insist. Baby steps. 
Agree
Agree
If by non conservation you mean non constrained hence subjected to neutral evolution, I agree.
Not sure this is true. In fact, it depends how you would define a new sequence that lands and fixes itself in the genome, for example by horizontal transfer. If you define such sequence as an unconserved part, then your assertion may be false. If you define it as unconstrained, I agree.
Only if 90% of the genome is unconserved in the sense that it is unconstrained. But is it the case?
Agree
Disagree.
The thing here is that under the design perspective, we have reason to think that most of the genome has a purpose. In Bayesian terms, P(E/A)>P(E/B), with:
E: most parts of the genome have a purpose
A: design hypothesis
B: naturalistic, blind, unguided evolution
And since, as an ID proponent, I think that P(A) >P(B), it follows that I have reason to think that P(E)>P(nonE).
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Right. So your reason to think this is a commitment to ID-proponent-ism. It’s not to do with the experimental data, it’s a matter of presupposing the thing and then, if push comes to shove, rationalizing the data away.
See, the problem is that whether it is actually the case that in this world most of the genome has a purpose or not is something that can be investigated independently of what ever perspective the inquisitor starts out with. When huge portions of DNA are meaningless repeats that never even could be expressed, because that would violate electrostatic restrictions on what amino acid sequences are physically capable of staying in one piece within the range of temperatures available naturally on our planet, let alone folding, the argument that “well, from my perspective, as an ID proponent…” is ultimately inconsequential. And when likewise huge portions of DNA can be completely cut out of a gamete, and that gamete still gets to grow into a viable organism which can even procreate, the argument that “well, you see, under the design perspective…” means absolutely nothing. It is not a matter of “perspective” whether E or ¬E is the case in this world. It is a question that can be experimentally investigated. And if we take at face value your reasonable assumption that P(E|A)>P(E|B), then we must conclude that P(A|¬E)\cdot P(A)<P(B|¬E)\cdot P(B).
Seeing as we seem to be living in a world where ¬E is the case, our choice is to accept it and see what else we can learn about it for our individual and collective benefits, or to forego reason and reasonableness, reject what nature seems to be unambiguously indicating to us, and try and function with fantastical beliefs instead, getting laughed at deservedly by our saner brethren until we have recruited enough ignorants to our ranks as to become a threat to them.
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The problem is you have no reason to be an ID proponent when it comes to our understanding of the genomes of organisms. There isn’t something about the data that needs one to invoke ID to explain what we see, where ID proponent here basically just means to be of the belief that essentially the vast majority of the genome is functional. It rather seems to be some sort of axiomatic belief, or a sort of lens through which everything you encounter is “interpreted”.
Curiously the mostly-functional view was predominant among most of the genome researchers that established the fields of genetics, genome research, and molecular biology, though they just invoked supreme optimization by natural selection as the reason why they thought this (the common rationalization was that natural selection would get rid of unnecessary stuff). These people eventually got convinced otherwise by their own research.
I think you should look into what it is that drives your view of the functionality of the genomes of most organisms, because it isn’t the data. You’re getting this view from something else and trying to make the data fit. But it doesn’t. Your hypothesis isn’t consistent with the data and you’re making up rationalizations for why the pattern you posit is actually absent. When you stick to a hypothesis not evident in the data then something else must be driving your adherence to the hypothesis besides the actual data and any explanation for it. What is that other thing?
I’m not sure any of the other stuff you said in this section means anything in the context of the human genome, but it doesn’t matter. Let’s just say that we are only taking about the unconstrained portions. I think the evidence suggests this is about 90% of the genome. If that number is wrong, I don’t care for the purposes of this discussion. Whatever the amount is, that’s the part we are talking about.
I’m not going to pretend to speak Bayesian. I don’t know what that stuff means. I’ll try and translate it into English to the best of my ability, and you can tell me if I get it wrong. What I understand you to be saying is that you think that you do have evidence of functionality in the unconstrained portions of the genome, and that this evidence is that it is a testable prediction derived from your hypothesis that the genome was intelligently designed. Is that fair?
If so, here is one of my concerns: I’m not arguing intelligent design with you. I don’t know whether the human genome was intelligently designed or not. There may be a god out there, who is guiding evolution, or who set things up in a certain way to produce a desired effect, or even who designed the genome de Novo when he created humans (I have my doubts about this last one, but leave those aside for the time being). But even if we assume there is a god out there who designed the genome, that doesn’t tell you anything about how he did it.
Maybe he designed the human genome in the same way that programmers designed alpha zero to play chess, that is, by setting up heuristics and relationships that can be tweaked, and then creating variations, having them play against each other, keeping the best ones, and repeating the process. This is still intelligent design. It resulted in the best chess engine that we have ever seen. It plays better chess than any of the ones designed deliberately. God could have designed the genome in some way that resembles that.
The point is, that just because the genome is intelligently designed, it does not follow logically that it will not contain junk. Junk may be a byproduct of the design methodology, and you have no insight into that design methodology, if for no other reason than because you do not understand the mind of God.
So, it does not follow that because you believe in a god, and you believe he designed the human genome intelligently, that this is a reason that it must contain little to no “junk”.
What you are really saying is that you believe that he designed the genome in such a way that there would be little to no junk, and therefore the genome contains little or no junk.
That’s not really a reason so much as it is a restatement of your conclusion, along the lines of:
“I think this is how it was done, which is a reason for me to think this is how it was done”
Do you see how that might be problematic?
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This is an assertion as any design that contains code rarely has junk code.
@Giltil inference is reasonable given what we know about designed sequences.
What I think is a more logical discussion is if the original design was many generations in the past then some junk could accumulate due to mutation.
English speakers refer to this as “dishonesty.”
A bold statement to make by someone who has never written code, never mind never having written the code for a neural network that undergoes deep learning. I’d ask you for your source, but you still owe me an answer on another topic, and I want that answer first.
Suffice it to say, you and I will discuss one topic at a time, and this is not our topic. Thank you for your help, but I think Gill is doing just fine on his own.
What we know about designed DNA sequences is nothing. Again, thank you for your contribution, but I am not interested in your assessment of what inferences are reasonable.
I am however interested in the answer to the very basic question I asked you.
We are not going to change the subject, but thank you once again for your input.
The subject is whether 90% of our DNA is junk.
At a minimum would it not be reasonable to explore one of the logical possibilities that the code initially starts fully functional at the time of an animals origin?
No, it would not be reasonable. I have no interest in such a flight of fancy. If you want to, go ahead. I’m sure we all await the results of your research with baited breath. Feel free to post your results to this forum.
That’s ok. Thanks for the conversation.
What does fully functional mean though?
Using phrases like “fully functional” implies the existence of some sort of functional optimum, but how would one even go about defining that to begin with?