Essentially everything Bill says can be addressed by linking to when someone corrected him the last time he said the same wrong thing. And 100% endorse this method of dealing with his nonsense.
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The explanation is very simple, too simple for you to understand, apparently. Can we agree that evolution with branching, inheritance, and changes would naturally result in a nested hierarchy? Let’s start there. This is true because species within a group inherit the changes that happened in the ancestor of that group, while species outside the group do not. Is that clear? I don’t know what rigor you would demand; it’s a simple and obvious consequence of common descent.
It’s impossible to talk to you, because there seems to be some entirely separate conversation happening inside your head, between you and some imagined version of other people. All I can say is that nobody so far has been able to think of another explanation. You certainly haven’t. “Common design” is not an explanation, just a buzz-phrase.
Depends. That question is answerable only given a specific scenario and model. But the good news is that we expect a data set that has lost all its information not to show a nested hierarchy, so we can detect when it happens.
This doesn’t this have anything to do with “reproduction and natural variation”, which just seems a repetition of your confusion between common descent and the causes of changes. What happens 30 minutes in is Buggs citing papers that test the existence of a tree and find that it actually exists, so it’s unclear why you’re pointing to it. Now, a few minutes later Buggs gives an example of gene tree discordance, which he then explains not by separate creation but by hybridization and incomplete lineage sorting. Nothing for you there. (I would suggest a third mechanism that seems very common in plants: unrecognized paralogy. Still nothing for you, though.) And note that Buggs never suggests or supports separate creation. I could argue with much of what Buggs says, but the more important point is that you don’t understand what he says and are just clutching at anything you can grope for that you imagine might help you, even though it actually doesn’t.
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Simple enough. The data used for phylogenetic analyses are not “similarity of regulatory networks” but the actual DNA sequences and morphological characters of the organisms. So everything you say there, dubious as it may be, is also irrelevant to phylogenetic analysis and to the hierarchical structure of the data actually used. I will point out that you also confuse similarity with nested hierarchy, and you confuse the hierarchy of a regulatory network with a hierarchy of character data, though there is no correspondence.
So you can’t delimit kinds, and you can’t give any reason to suppose even that one should suspect any taxon is a created kind.
More word salad. No prediction of convergent evolution is involved, only the observation of convergence, and that’s possible only because the same event is seen to happen in two spots on one tree.
Those are not predictions. They’re observations. Predictions would be “I predict that there will be convergent amino acid changes in these particular genes”, before looking at the genes. Nothing of that sort happened.
Such experiments would not in any way test what you claimed were predictions. Note, by the way, that these observations are not of HGT, just evolution occurring within homologous genes.
There’s nothing to respond to. You have mistaken the hierarchical structure of a regulatory network for the hierarchical structure of the data we use for phylogenetic analysis, and there is no connection between the two. You just find particular words used in some passage but don’t read or understand the text in which those words are embedded.
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@Tim looks at @Meerkat_SK5’s further serving of ignorant, arrogant, malformed blather.
Going down this rabbit-hole of his endless argumentum ad nauseam any further is neither productive nor entertaining.
I will leave him to his delusions of competence.
¯\_(ツ)_/¯
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What changes do they inherit? Mutations to existing genes?
Thats right and similar to what we see in vertebrates. How does common descent produce a pattern where different genes produce different trees?
It doesn’t matter what the changes are as long as they’re heritable. Any heritable alteration of the genome will do. Changes to existing genes, changes to non-genic sequences, deletions, insertions, inversions, whatever.
Not true. Vertebrates show much less discordance than in Buggs’s example.
I’ve already told you, and so in fact did Buggs if in fact you had bothered to pay attention. There are many ways in which one can get gene trees discordant with each other: noisy sequences that don’t strongly support anything; short internal branches; poorly chosen models or methods of analysis; incomplete lineage sorting; unrecognized paralogy; horizontal transfer, including hybridization, introgression, transfection; convergence. All these can be distinguished by examination and analysis of the data. In aggregate they are seldom enough to confuse an analysis if there’s enough data.
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Try starting where @John_Harshman suggests starting by answering that simple question.
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All these with the exception of gene convergence are possible explanations if you ignore the problem of time to fixation of changes to a population generating new genes.
There is no reconcilable theory here that can point to a single origin event.
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There is no such problem. You keep claiming there is, and then refuse to show your math. Until you can show your math, continuing to claim a problem exists is just a lie.
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Once again, your central blind spot is your inability to separate common descent from the causes of mutation and fixation. If there were indeed a waiting time problem (there isn’t), it would be evidence for some kind of divine intervention in causing particular mutations or in helping them increase in frequency, but it wouldn’t affect the inference of common descent based on nested hierarchy.
So why no waiting time problem? Well, for one thing, most of the genome is evolving neutrally, and only a tiny proportion of mutations ever become fixed. There are just so many in the genome that some reach fixation, by chance, in every generation. Nobody is waiting for anything, and you’re suffering from the Texas sharpshooter fallacy. But again, none of that is relevant to the evidence for common descent.
Say, could you try answering the question: “Can we agree that evolution with branching, inheritance, and changes would naturally result in a nested hierarchy?”
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Do you not see how vague this question is? What changes? With this process can we look at a population of sisters generating a population of children and grand children with cousins and second cousins and generate an accurate tree with genetic data?
John, the problem is you are trying to force fit a model of a single origin event when the data does not support the hypothesis anymore.
If God is involved in the change that is by definition a separate origin event as reproduction and natural variation cannot explain it.
No. It’s a simple, direct question. The nature of the changes is irrelevant, as I have explained to you countless times. Why won’t you answer?
Yes, if we gathered enough data. But you would need whole genomes, more or less, because the sisters would differ by only a hundred or so mutations.
How would you know? You’ve never so much as seen any of the data.
That’s not the definition. Once more you confuse common descent with the cause of changes. The causes don’t matter as long as the changes happen on a tree of descent.
We can use haplogroups as an example of the output of reproduction with inheritance and variation.
Wikipedia - Haplogroup, bold mine:
Each haplogroup originates from, and remains part of, a preceding single haplogroup . As such, any related group of haplogroups may be precisely modelled as a nested hierarchy in which each haplogroup is also a subset of a single broader set
As John has aptly explained, the nested hierarchy is equivalent to a branching tree.
That is a theological question. On what basis would you constrain the miraculous?
Much of the nested hierarchy we find in nature, both morphological and genetic, is arbitrary and serves no evident teleological purpose. Conversely, nature’s solutions to common functional requirements, such as bat wings and bird wings for flight, or whale flippers and shark fins for hydrodynamics, demonstrate ancestral adaptation. Thus, convergence does not show common design, but rather demonstrates common descent.
If fiat creation is indistinguishable from common descent, what you have is the omphalos hypothesis along with its theological objections.
Actually, it is more of a inherent procedural output than a prediction. Certainly, it is not a rhetorical argument.
Then the claim of common descent is meaningless at best and deceptive at worst. Be clear you are claiming simply that there are similarities among animals nothing more.
The Venn diagram indicates multiple origin events. If God is involved it is a separate origin event.
Common descent implies (to the public) that we can explain the observed tree with reproduction and natural variation alone.
Then, I will explain it in a way that is more relevant. The genetic code is nearly the same for all living organisms, and variations in the code are responsible for differences in traits between organisms. As organisms evolve and diversify, the genetic code is inherited and modified through a process of HGT, resulting in the formation of new species and groups of organisms.
This process of HGT creates a nested hierarchy of organisms based on their shared design and the extent of their genetic similarities. Organisms that share more recent common design will have more similarities in their genetic code and will be grouped together in smaller, more closely related categories, while organisms that diverged from a common design further back in time will have more differences in their genetic code and will be grouped together in larger, more distantly related categories.
No, I am saying you can’t delimit kinds based on only one analysis.
I think you misunderstood me here or I don’t understand your objection. Let me bring more clarity.
There is a four-question survey where each practical criterion is designated by a letter (A–D) and a title in the form of a question (relating to food, predators, reproduction, and habitat).
For example, if the answer to the question “Is the common feature of this group being used differently in their habitats?” is “No,” “To be determined (TBD)," or “Not applicable (N/A),” a follow-up question is asked: “Do they respond differently in different habitats?” This may require artificially planting them in different habitats for an answer.
Based on the first panda study, the answer to the first question is “Yes,” :
“the false thumb of the giant panda probably evolved for manipulating bamboo, the false thumbs of the red panda and of S. batalleri more likely evolved as an aid for arboreal locomotion, with the red panda secondarily developing its ability for item manipulation and thus producing one of the most dramatic cases of convergence among vertebrates”.https://www.pnas.org/doi/full/10.1073/pnas.0504899102
If this is true, I predict that there will be convergent amino acid changes in these particular genes DYNC2H1 and PCNT or HOXC10 and HOXC1
That is not true. The researchers in the panda study made these predictions regarding the genetic basis of this convergent evolution, including:
Genes involved in the digestion and metabolism of bamboo would be under positive selection in both the giant panda and red panda genomes.
Convergent evolution would be more pronounced in genes related to bamboo digestion and metabolism, compared to other genes.
You are actually right. They would just confirm the roles of those genes in question.
Here are the methods that actually detect convergence according to the panda study:
Site-specific likelihood ratio tests (SLRTs): The researchers used SLRTs to compare the rates of evolution at different sites in the protein-coding sequences of candidate genes. They looked for sites that had undergone convergent evolution in both giant pandas and red pandas.
Branch-site models: The researchers used branch-site models to detect genes that had undergone positive selection specifically in the lineages leading to giant pandas and red pandas. Positive selection can be an indicator of adaptive evolution and convergent evolution.
Molecular evolutionary analysis: The researchers analyzed the rates and patterns of molecular evolution in candidate genes to look for evidence of convergence. They compared the levels of similarity and divergence in the genes between giant pandas, red pandas, and other mammals.
I beg to differ. The common design model predicts that over 80% of taxonomical groups have functional ERVs and pseudogenes because the mechanism the designer uses in the form of HGT yields this effect inherently (See the competitive endogenous RNA hypothesis)… HGT also produces rapid evolutionary changes, which is why we would expect those same genes to show signs of rapid evolution.
And this is irrelevant to my point I made earlier. Again, we would expect to see nested hierarchies emerge when similar parts and functions are adapted to fit and fill different environmental niches.
You dismissed this and claimed that this would not be the case. In contrast, you just acknowledged that the study I gave you does confirm that this common design process would produce nested hierarchies.
I think you were probably thinking that common design theory was logically dependent on the HGT mechanism being true, but it is not. They are independent from each other just like natural selection and common descent.
Owen advocated for saltations and separate creation. So we would anticipate a mechanism that could produce the same effect, which would be HGT. But, HGT is just an example that supports the theory.
Again, whatever tests you may have would need to be related to my theory or the Orch-OR model.
Yes, thank you for conceding my points.
I beg to differ.
Both common design and common descent can and have explained the same data for decades now. The difference between the two is that common design can be directly tested and there is independent evidence in support of it. The same CANNOT be said for common descent theory. This is why there is no evidence for it outside of your imagination.
It is time to actually support your claims Ron and Roy
No. You know nothing. This isn’t about similarities. Nested hierarchy is not just “similarities”. Apparently the reason you won’t answer the question is that you can’t understand the question. You have a mental block against comprehension, for some reason.
Neither of these claims is correct. You don’t have any idea what the Venn diagram indicates. If God is involved he may have introduced new genes (though in most cases curiously similar to old genes or non-coding sequences), but they were apparently introduced into a chain of descent.
Why should we care what it implies to the public, even if you were correct about that?
Nope. Not true in any way. Variations in the code have nothing to do with differences in traits. I think the two parts of that sentence assume two different meanings of “genetic code”, and only the first is correct. At any rate, you can’t change meaning in the middle of a sentence.
Nope. The genetic code is not modified by HGT, and modifications to the code do not result in the formation of new species and groups.
That would not in fact create a nested hierarchy.
Even assuming you were right about the genetic code, why would more recent common designs have more similar codes? And do you even know what a nested hierarchy is?
But I asked how you can delimit kinds, not how you can’t. In particular, I’m asking how you know that the two pandas belong to different kinds, what those kinds are, and how you know.
The survey questions are meaningless and arbitrary, and there is no reason to expect the answers to delimit kinds. Please stop thinking that merely cutting and pasting the same text multiple times is clarification.
So? How does that make them separate kinds?
That’s not a prediction, since you already knew those changes existed. Further, you have no reason to make statements about those particular genes except that you already know they have convergent changes. You don’t know what prediction is.
Where exactly do these predictions occur in the study?
How were candidate genes chosen?
You beg mistakenly.
That’s just nonsense. There is no such prediction and pseudogenes are not the result of horizontal transfer, though you could argue that ERVs are.
Not true. HGT is a rapid evolutionary change. It doesn’t necessarily produce rapid sequence evolution. It’s selection that would do that.
Ah, but we wouldn’t. There is no reason to suppose such a thing.
Not true. For one thing, that wasn’t common design. For another, it wasn’t a nested hierarchy among species but among downstream influences in a single regulatory network. Not comparable in any way.
No, I wasn’t thinking that. Of course there is no such thing as common design theory, just various sets of vague, ad hoc notions held by various creationists.
Did Owen actually advocate for separate creation? Of what? Where? And of course HGT does not produce the effect of nested hierarchy. There is no support for the “theory”.
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No creationist organization would agree with this. Not AiG with its created heterogeneity, not CRS with its CET continuous environmental tracking . Do you really think that giraffes and okapi’s diverged due to HGT?
Beg away.
Yeah, maybe I think that your incoherent quantum woo and HGT ramblings speak for themselves, and there is no value in further engagement. No journal, even BIO-Complexity, will publish this mess. Go ahead and prove me wrong.
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Have you considered the possibility that there might have been many origin events, but all of them are ancestral to the life that we find today?
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You could write down everything relevant Bill has considered on a postage stamp and have room left.
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