The Argument Clinic

Note that you cited a paper on ichneumon wasps that had nothing to do with carnivorous activity. And Darwin’s point about the wasps wasn’t about predation, per se, but about the cruel details of the particular form of predation.

I repeat: Owen believed in archetypes, and Owen was a saltationist, but those two ideas are not in any way connected. Neither follows from the other. Also, sudden changes presuppose common descent, which you deny. Your repeated quote says nothing relevant to your claims.

If it makes no predictions about the fossil record, what have you been blathering about all this time?

Yes we do. There’s abundant evidence for the common descent of different orders and families. What you say hasn’t been looked at has indeed been looked at. Nor does similarity of ecology imply common design rather than common descent. Your criterion is worthless.

Sorry, but Hugh makes no sense. He has no clue what he’s talking about there. In fact supernatural intervention explains nothing, because it just supposes that “God made it that way because he wanted to”, with no expectation of what would or would not be observed.

You have already (above) said that your model “does not make specific predictions about the fossil record”. Which is true? Prediction or no prediction? And again you fail to confront the actual pattern, stasis and punctuation within species but not between higher taxa, and it’s the latter your notions demand.

I see no evidence of such a thing. Nor does that seem relevant to your model, such as it is. Now, what high amounts of gene-tree conflict result from bursts of speciation, i.e. many splitting events in an evolutionarily short time, the sort of thing expected from an adaptive radiation. And an adaptive radiation might also result in considerable morphological evolution. But the two are not otherwise connected.

I am not. Inductive reasoning relies on the evidence to support an argument being a unique expectation of the hypothetis being supported. But you present irrelevance. Nothing you present as evidence ever actually supports what you claim, and most often it has no relation at all except for a few of the same words.

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I will confess that I don’t understand this at all. Why wouldn’t 25 or 30 or 40 amino acids work as well?

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Balderdash!

Shear mangled, incoherent, ignorant, meaningless nonsense!

The phrase “universal self-collapsing genetic code” is simply the meaningless word salad that comes from juxtaposing lack of meaningful understanding of quantum physics with lack of meaningful understanding of genetics. The suggestion that this non-existent “universal self-collapsing genetic code” could be a “Universal common designer” is ludicrous.

Kindly stop wasting our time with this ignorant drivel!

Tim’s Universal “Universal” Theory

Any time @Meerkat_SK5 uses the word “universal” in a statement, it will have no scientific substantiation.
Examples:

  • Universal common designer
  • Universal self-collapsing genetic code
  • Universal proto-consciousness field
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By way of an experiment, I asked ChatGPT “What is a universal proto-consciousness field?” and got the reply:

The concept of a universal proto-consciousness field is a theory that suggests that there exists a fundamental field of consciousness that pervades the entire universe and serves as the source of all individual conscious experiences. This idea is often associated with spiritual and philosophical beliefs, but it has not been scientifically proven and is not widely accepted within mainstream science. The notion of a universal consciousness field remains largely a matter of speculation and is not supported by empirical evidence.

“What is a universal self-collapsing genetic code?”

I’m sorry, but I’m not familiar with the term “universal self-collapsing genetic code.” It doesn’t seem to be a well-established or widely used term in science. It’s possible that it refers to a theoretical or speculative idea that has not yet been validated by scientific research, or it could be a term used in a specific subfield or discipline that I am not familiar with.

In general, genetic code refers to the way in which DNA or RNA molecules encode the instructions for making proteins, which are the building blocks of life. The genetic code is considered to be universal in that it is nearly the same in all living organisms, from bacteria to humans. However, I have not come across the term “self-collapsing genetic code” in my training data.

“Do quantum search algorithms explain why there are four bases and 20 amino acids in genetics?”

Quantum search algorithms, which are based on quantum mechanics principles, can be used to search through large data sets much faster than classical algorithms. However, they do not explain why there are four bases and 20 amino acids in genetics.

The number of bases and amino acids in genetics is a result of the specific biochemistry and evolution of life on Earth. The four nitrogenous bases in DNA (adenine, guanine, cytosine, and thymine) were chosen because they can hydrogen bond with each other in a specific way to form the double-stranded DNA helix. The 20 common amino acids in proteins were selected through evolution because they are able to form a variety of structures and perform a wide range of functions.

In summary, the number of bases and amino acids in genetics is not related to quantum search algorithms, but rather to the biochemistry and evolution of life on Earth.

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This is not true.

This is not entirely true.

This assumes that they were chosen, which does not appear to be the case.

Patel’s article must be about as useful as one that explains why elephants can fly.

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Now, I am pretty confident you did not read much of my paper. I will have to summarize a part of it then:

DNA contains two types of information: digital, represented by genetic information, and analog, represented by the genome; both are present in DNA and have many properties almost identical to those in man-made computers and linguistic texts.

Based on this data, God probably operated in a similar manner to humans when designing life on Earth. This means that we would not have to worry about using an unfalsifiable theory that involves an omnipotent human because a non-computable being like God cannot violate his own nature.

In other words, the non-computable trait that this designer possesses offsets the omnipotent trait that this designer would also have to possess if this is true. For this reason, we would expect God’s human nature to be consistent without the flaws that humans naturally have because of their inherent physical limitations.

This allows us to treat an omnipotent God in the same way we would treat other intelligent agents (Neanderthals, modern humans, extraterrestrial intelligence, etc.) when we want to use a valid cause to explain a biological phenomenon over a mindless force.

Thus, all candidates are considered natural but immaterial causes that we can test because consciousness is supposed to be fundamental physics not classical physics.

Let me refresh your memory again then:

“Organisms that frequently exchange genes become more similar, and transfers between these groups may then be categorized as HGTs with a bias reflecting overall relatedness, even though the initial transfers may have been biased by other factors. We have previously shown that biased gene transfer CAN CREATE and maintain phylogenetic patterns that resemble the signal created through vertical inheritance .” [emphasis added]

Biased gene transfer and its implications for the concept of lineage (nih.gov)

Horizontal regulatory transfer (HRT)

I seriously doubt this is what I was referring to because I don’t even know what you are talking about. You are going to have to elaborate on your point because I rather not guess.

Again, I’m not following you. What is your point? What are you getting at? What does this have to do with what I was explaining to @T_aquaticus? Or do you not understand the point I was making to him?

Actually, I was not trying to make a point or claim, but was trying to understand @Dan_Eastwood’s point better by inquiring more information when I said…

You mean no atheistic researchers would think it has any worth. But, what makes you think Christian researchers would feel the same way?

Then, I said…
I am not sure what you mean by that. For instance, Paleontologists would obviously not think this framework could lead to successful research for their work because it is not in their field of expertise.
So how could it be the same for everyone?

Also, when I asked these questions, I was referring to the emotional side of it, primarily.

Sorry, I gave you the wrong study:

pnas.org/doi/10.1073/pnas.1115133109

That’s more of an aesthetics argument against it not a scientific one.

But you suggested that saltations theory is not part of his archetype theory, which is false. And I never said one follows from the other. Instead, I am saying Richard Owen put the two ideas together in his theory:

"Owen’s Platonism, as we have seen, is fully compatible with Cuvier’s fragmentation of the Great Chain of Being into diverse “embranchments,” placing new emphasis on individual species. Upon this structure, Owen was able to superimpose his theory of archetypes and other modifications which had been formulated to explain the lacunae in the chain’s continuity [7].

Owen explained that each section of the chain had its own archetype and does not have to be temporally complete. Certain intermediate species may exist either in the past or the future: ‘The possible and conceivable modifications of the vertebrate Archetype are far from having been exhausted in the forms that have hitherto been recognized, from the primaeval fishes of the Paleozoic ocean of this planet up to the present time.’

https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.923.6553&rep=rep1&type=pdf

Yes, based upon your model and methods. But, based on our model and methods, we have a lot of preliminary results suggesting that many different orders and families evolved separately:

A List and Bibliography of Identified Baramins | Journal of Creation Theology and Science Series B: Life Sciences (coresci.org)

No, this is not the ecology criteria I described before anymore. I made many changes to the method. Let me describe it to you again:

We can assess the prediction by applying analogous phenotypic traits between families and orders to different environmental niches based on similar needs.

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. If the answer to either question is “Yes,” we can start testing whether there are adaptive and structural convergent genes pertaining to the application of this analogous trait. If the test reveals at least one adaptive and/or structural gene, we can confidently conclude a common design.

However, if the answer to both questions is “No” or “TBD,” we must apply the same question formula to prey and/or predator measures to potentially draw a definite conclusion. If the answer is still “No” or “TBD,” then we ask, “Is the common feature of this group being used differently in sexual reproduction?”

The results are inconclusive if every question yields a “No” or “TBD” answer. This method was inspired by a study on red and giant pandas, which concluded that their false thumbs evolved separately in response to similar needs, [50] and a study that showed why and how they evolved separately. [51]

[50] Evidence of a false thumb in a fossil carnivore clarifies the evolution of pandas | PNAS

[51] Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas | PNAS

Hugh ross is an advocate of Richard Owen’s theory. So “supernatural intervention” to him is just considered to be saltations theory.

Yes, my model and predictions ,which are emanating from Richard Owen’s theory, does not . But, Richard Owen’s saltations model of the fossil record does, which he combined with his archetype theory. Just read the first 9 pages of this article, which he created after his archetype theory. It describes these splitting events in more detail:

On Parthenogenesis; Or, The Successive Production of Procreating Individuals … - Richard Owen - Google Books

That is because you did not read my entire article. I was merely copying and pasting what I wrote in my article. You should just read the rest of the article so you can better understand the context of what I was trying to convey.

It looks like this article explains why…

Why twenty amino acid residue types suffice(d) to support all living systems - PMC (nih.gov)

I’m willing to call it: Byers’ Point™ reached.

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Is there a formal definition of your “Byer’s Point”? Or is it merely the point at which the resemblance to Robert Byers becomes obvious. (Also, shouldn’t it therefore be “Byers’ Point”? :slight_smile: )

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The Byers’ Point™ is the point at which the absurdity of a position has gone hopelessly off the rails and all efforts of restoration to the realm of reason are futile. Yes, I coined it in honor of the allegedly indomitable Robert Byers when he was still frequenting PS.

Indeed it should. Unfortunately, I was using a junky bluetooth portable keyboard with an Android tablet and the keys alternate between not working and repeating, so I constantly have to backspace to try to edit what I just typed.

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That was no different from your ordinary practice. And the “right” study is also irrelevant to the point.

Of course it isn’t a scientific argument. It’s a moral argument. Either God didn’t cause this, or God is cruel and immoral. Which would you prefer?

What evidence do you have that it’s false? As usual, what you quote and cite doesn’t say what you think it does.

Again, what you cite doesn’t say what you think or support what you claim.

Much too vague, so much as to be non-operational. Further, there is no attempt to justify the criteria as delimiting a kind or basic type or whatever you think you’re talking about.

Nope. Hugh Ross, last time he said anything, thought that every species was a separate creation. No saltation; that requires common descent.

You have no model. You have no predictions. And your understanding of Owen’s views is poor. And “does not” what?

What “splitting events”?

You should stop doing that over and over. Now, in a scientific paper, a reference is supposed to support the statement in which it is cited. “The rest of the article” is not relevant.

Not really, and it appears to be a completely different explanation from what’s hinted at in your previous source.

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But Byers, at least, managed to get his article published somewhere.

Post-Flood Marsupial Migration Explained – Revolution Against Evolution (rae.org)

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How so?

No, aesthetic and moral values are not same thing:

Many philosophers, beginning with Plato, have classified aesthetic and
moral judgments together on the basis of one important, shared feature: both
involve value judgments. This practice is misleading, as these two forms of
judgment can be very different; for instance, moral judgments always imply
obligation and the compulsion to act in certain ways, features that are not
necessarily present in aesthetic judgments.
Microsoft Word - KAJH art 2-edited.doc (usm.my)

With that said, what about that act is considered to be immoral to you? It can’t be the death or pain part, is it?

I will just go back to the same article, but this time I will only show you furhter details and highlights in it that should hopefully show you why you are grossly mistaken here:

He was a strong advocate of the notion that the paleontological record is progressive… For Owen, this progressive change was a process guided by divine purpose. He believed in an orthogenetic-saltational process of organic unfolding, driven by an inherent tendency to change…

The phenomenon of metagenesis provided Owen with a visualizing aid for his notion of evolution. In the booklet On Parthenogenesis, or the Successive Production of Procreating Individuals from a Single Ovum (1849), he described the phenomenon of alternating generations in the reproductive cycles of, for example, aphids, jellyfish, or flukeworms. …One could imagine that under particular circumstances the cycle might be broken, and the separate stages go on reproducing. In this way wholly new species might originate.

Owen applied his saltational theory of the origin of species also to humans and stressed the unity of mankind and the gap that exists between humans and the higher apes. Based on a series of comparative studies of the anthropoid apes, he placed humans in a subclass of their own, the Archencephala , pointing to a number of specific cerebral features, in particular the hippocampus minor .

This method was inspired by a study on red and giant pandas, which concluded that their false thumbs evolved separately in response to similar needs, and a study that showed why and how they evolved separately.

So the two-step ecology criteria are operational and validated by previous studies. I am merely combining the methods from each study into one.

Origin of life and species model

Approximately 3.8 billion years ago, pi electron resonance clouds in single-chain amphiphile molecules coalesced in geometric pi-stacks, forming viroids with quantum-friendly regions for OR events within Earth’s deep-sea hypothermal vents. [45]

Subsequently, through natural selection and OR events, groups of viroids formed into highly ordered local domains of key biomolecules of a DNA/RNA virus or molecule, which later evolved into different species of unicellular organisms. [46]

Through HRT, these unicellular organisms underwent extensive regulatory switching and rewiring in their noncoding regulatory regions, which led to the divergence of transcription start sites and gene expression levels in the formation of primitive multicellular organisms. This same multicellular toolkit and modules of slime molds then developed into created kinds at different times and global locations (for more details, read Stuart Hammeroff’s description of how microtubules played a part in the origin of species). [5]

Origin of species predictions

Based on this theory, we would expect to find:

(A) Over 80% of families and orders evolved separately.

(B) Over 80% of ERVs and pseudogenes are functional.

(C) The regulatory regions of core gene promoters between families and orders are over 50% incongruent with species phylogenies (i.e., vertical inheritance).

How? Because it fails to discuss anything relevant to the point. In the same way that the Treaty of Ghent is irrelevant to the Boxer Rebellion.

Nobody claimed they were. You just mistook the subject.

Did you even read the Darwin quote that started this up? Why do you grossly misunderstand everything you read?

OK, I see how there is splitting referenced. But there seems nothing to do with archetypes. And I point out again that this is antithetical to your notions of separate creation.

So what? that’s just convergent evolution, easily seen because giant pandas are bears while red pandas are not. One thing they most certainly are not is unrelated by descent. Nothing to do with your “method”, which is just incoherent. You can’t justify it as leading to separate basic types by reference to species that are clearly related by descent.

Still just as incoherent as it was the last time you brought it up. Nor do your “predictions” follow from your “model”. But let’s look at them in their own terms.

Already falsified by phylogenetic analysis.

Clear evidence against this claim: almost all are evolving neutrally.

It’s not clear what that “prediction” even means or what the data should look like in order to test it.

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Forgot to point out that Owen was wrong about nearly everything related to evolution, but it’s particularly amusing that your quote ends with mention of the hippocampus minor. I can’t seem to find that passage in what you claim to be your source. Have you perhaps quoted from another secondary source? And are you acquainted with Huxley’s dismemberment of that particular claim of Owen’s?

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I guess I don’t know what your point was or what you wanted to know.

Oh, I think I see what you were asking for now.

" I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae [parasitic insects] with the express intention of their feeding within the living bodies of Caterpillars.”

If Richard Owen’s theory is true, the ecosystem of caterpillars will balance out and stay at healthy levels when researchers add the Ichneumonidae to the mix.

The archetypes that Owen’s is referring to would just be the genetic code according to modern science. So it has everything to do with archetypes because these reproducing cycles would not be reproducing without this universal genetic code/archetype.

I don’t see how. Again, the article pointed out that the "phenomenon of alternating generations in the reproductive cycles of, for example, aphids, jellyfish, or flukeworms. …One could imagine that under particular circumstances the cycle might be broken, and the separate stages go on reproducing . In this way wholly new species might originate. "

In other words, each start and end of a reproductive cycle represents a separate creation.

Both models explain convergence differently though.

For instance, the common design model views convergence as resulting from a universal common designer who employs a single, optimal solution to address a common set of problems faced by organisms possessing different characteristics and living in different habitats.

Common descent views convergence as occurring when unrelated species encounter identical, or nearly identical, environmental, predatory, and/or competitive selection effects. In other words, common descent suggests that natural selection channels randomly occurring variations in unrelated species toward identical outcomes.

There are two obvious problems with the common descent explanation for convergence. First is the frequency with which it is observed to occur. Second, occurrences of convergence where the environmental, predatory, and competitive selection effects would not at all be similar.

You seem to be incapable of separating the concept of common descent and nested hierarchy. They are not synonymous. The HGT and common blueprint the designer used is what produces those same patterns and equally explains it.

It has everything to do with it based on the definition I provided:

Definitions

Common design: To create and develop animals through the common process of HGT for the common purpose of surviving, reproducing, and pioneering different environments.

Universal common designer: universal self-collapsing genetic code shown by the shared DNA among all living organisms (i.e., objective reduction).

We can test this by applying analogous phenotypic traits between families and orders to different environmental niches based on similar needs.

The ecology criteria I mentioned is crafted according to these definitions, which is also justified by the two panda studies.

Further, what makes both models different is that you guys merely assume that those analogous traits came from a common ancestor without testing it.

Again, common descent and nested hierarchy are not synonymous and common design can explain those patterns just as well. So we still don’t know yet.

I beg to differ. The competitive endogenous RNA hypothesis as a comprehensive model for pseudogene function presents an elegant framework to explain the function of all members of the category. This type of advance coheres nicely with the catalogue of functional elements ENCODE identified.

It is based on this study:

“analysis of the genomes of 46 sequenced isolates of Escherichia coli provided a statistically supported comparison of the phylogenetic tree topologies for regulatory regions, their regulated genes, and vertical inheritance. The results of this comparison highlight the notion that the evolution of regulatory regions of over half of the core genes (i.e., genes shared by all isolates) was incongruent with that of vertical inheritance.”
https://www.pnas.org/doi/full/10.1073/pnas.1413272111#abstract

I am predicting that this will be the case for families and orders as well.

Yes I have heard about it.

Just read the section “Hippocampus controversy” at the end of the same source:

True. Just don’t try to put the responsibility for your ignorance on me.

What does any of that have to do with Owen? And simple predation would have been enough to balance the population, without any need to eat the living caterpillars gradually from within. You still seem to have no comprehension of the issue here.

No, the genetic code is not an archetype. The genetic code is the mapping of 64 DNA/RNA triplets to the 20 amino acids. Nor is the archetype the genome. You are, as usual, spouting gibberish.

That’s not “in other words”. That’s you misreading as usual. Owen is talking about such things as neoteny, in which larval morphologies reproduce. Like axolotls, for example. Is an axolotl a separate creation from a salamander? If so, you have destroyed the meaning of “separate creation”.

The common descent model explains it. “Common design” explains nothing.

And yet the designer seems to employ quite different optimal solutions in different taxa. Remember the vertebrate eye vs. the cephalopod eye? One might also ask why pandas don’t have real thumbs and had to be supplied with replacements.

What frequency is observed, and why is that too high for common descent? What occurrences of covergence are you talking about in the second case?

I’m afraid you are incorrect. Neither of those is expected to result in nested hierarchy, but of course it’s the central expectation of common descent. Therefore nested hierarchy is evidence for common descent rather than common design.

Your definitions are incoherent. Please stop just repeating the same nonsense. Ref: Einstein’s (perhaps apocryphal) definition of insanity.

Nope. The very panda studies you cite show how convergence can be tested. The reason you know they aren’t homologous is that the two pandas do not form a clade of panda’s-thumby species.

Ah, but they can’t. You just declare that common design produces nested hierarchy. You have given no reason why it should.

ENCODE didn’t identify functional elements. It identified elements with particular sorts of biochemical activity that are known to occur at high frequency in random sequences. That’s evidence of nothing. And I see you have ignored the evidence for the existence of junk.

It would be easy enough for you to test that. But it certainly isn’t true for animals, especially if you claim, as you do above, that most of the genome is regulatory.

Thank you for finally providing a source, though you appear to have mixed at least two different sources. So you agree that Owen was quite wrong about humans belonging to a separate archetype from other primates?

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What do you mean. It is your point. Don’t you want me to understand it so I can address it properly?

Remember what I said before, a scientific theory is a large overarching well-tested explanation that unites lots of fields and explains lots of different kinds of observations. What springs forth from there are hypothesizes that are narrow and we can test it.

Richard Owen’s universal common design/archetype is that overarching theory and is based on the God of the bible.

What springs forth from there is the hypothesis God is omnibenevolent and designed animals for the purpose of surviving, reproducing, and/or adapting. For this reason, God will not design animals with pathogens or features that reduce the population or another animal’s ability to survive, reproduce, and fit an environmental niche.

I was just showing you a way to test the theory from that example. That is what you wanted I thought.

The archetype is just referring to the abstract blueprint that we refer to now as the genetic code or wave-function.

I will convey my point through Stephen Jay Gould’s article:

" the entire geological history of vertebrates may be interpreted as a movement towards humanity, guided by natural forces ordained by God as secondary causes. Owen’s oft-quoted last paragraph provides a genuine expression of evolutionary views in this limited sense (transformations within an archetypal framework under unknown, but natural, laws established by God to implement His plans of progress)…"

“…Owen regards an archetype as a blueprint of myriad possibilities (made all the more intelligible by limiting their range to products of common elements in unvarying topological order). All realized examples on earth therefore include only a small subset of possible forms. Owen even felt free to speculate about the anatomy of life on other worlds, provided that the vertebral archetype can lay claim to universal status”.

From the article I gave you before:

“Owen applied his saltational theory of the origin of species ALSO to humans and stressed the unity of mankind and the gap that exists between humans and the higher apes.”

As you can see, his saltational theory involved separate creation of animal groups, which included humans according to that article I gave you. Again, you are mistaken.

It seems that way but it is not that way. Again, every living creature on Earth uses the same code, in which DNA stores information using four nucleotide bases. The sequences of nucleotides encode information for constructing proteins from an alphabet of 20 amino acids.

This means that if we replay the evolutionary history of life, it will lead to identical or nearly identical outcomes.

A study by biologists demonstrated, at the molecular level, that evolution is both unpredictable and irreversible. The study focused exclusively on the type of evolution known as purifying selection, which favors mutations with no or only a small effect in a fixed environment. This is in contrast to adaptation, in which mutations are selected if they increase an organism’s fitness in a new environment. Purifying selection is by far the more common type of selection.

Contingency and entrenchment in protein evolution under purifying selection | PNAS

One example would be the centralized nervous system found in all vertebrates and insects.
Convergent evolution of bilaterian nerve cords | Nature

Not true, common design or HGT produces and explains the same patterns better:

A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes.

https://www.pnas.org/doi/abs/10.1073/pnas.1205856110

" we statistically tested for incongruence between the topology of the promoter sequences against the species tree. The null hypothesis of this test is vertical inheritance (as defined by the species tree); therefore, rejection of the null hypothesis is a strong indication of HRT. We found that 51% of all core gene promoters are incongruent with the species phylogeny, indicating that regulatory regions, similar to coding genes, are frequently transferred. " Transfer of noncoding DNA drives regulatory rewiring in bacteria | PNAS

“Because of the critical tasks of translation elongation factors, it is widely believed that EF-1α/EF-Tu genes have been vertically inherited from the last universal common ancestor (35), and the gene products are ubiquitous in all extant cells. However, large-scale sequence data from phylogenetically diverged organisms started unveiling cases that clearly violate the above preconception about EF-1α/EF-Tu evolution.”
Direct phylogenetic evidence for lateral transfer of elongation factor-like gene - PMC (nih.gov)

“Organisms that frequently exchange genes become more similar, and transfers between these groups may then be categorized as HGTs with a bias reflecting overall relatedness, even though the initial transfers may have been biased by other factors. We have previously shown that biased gene transfer CAN CREATE and maintain phylogenetic patterns that resemble the signal created through vertical inheritance .” [emphasis added]

Biased gene transfer and its implications for the concept of lineage (nih.gov)

Ok, but the panda studies were a two-step testing process. In the first study, they applied the false thumb to different environmental niches based on similar needs, which confirms the common design model. in the second study, they compared the two genomes to show how they evolved separately.

How would you construct the first part of the test for the common descent model? It would have to be constructed in a way that shows how natural selection channels randomly occurring variations in unrelated species toward identical outcomes. Otherwise, Common descents explanation of convergence can’t differentiate itself from common design.

How would you test that? What are the criteria to go along with comparing genomics between the two families?

Until you construct your own method, it is not testable.

That can’t be true. For instance, a study showed that high affinity non-functional binding sites are rare:

“In this study, we analyze DNA-binding proteins in 947 bacterial or archaeal genomes and the genomes of 75 eukaryotic species…Our analysis demonstrates that weak binding sites in genomes are preferentially avoided, a result that holds true across the domains of life. Put another way, we show that the global word composition of each genome has been molded by its DNA-binding proteins over the course of evolution.”

Phys. Rev. X 6, 041009 (2016) - Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales (aps.org)

As you can see, if most of the binding was random it would mess up the process of gene regulation because random interactions among genome components would potentially be very deleterious to the organism. Without minimizing these disruptive interactions, biochemical processes in the cell would most likely grind to a halt. This means that most of the binding that was measured by the ENCODE project was probably functional binding.

In fact, a study by Harvard scientists indicated that the concentration of PPI-participating proteins in the cell is also carefully designed.

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions | PNAS

As Fuz Rana has further suggested and pointed out, “high-precision structures and interactions, exemplified by PPIs, are hallmark features of biochemical systems and, by analogy to fine-tuned human designs, point to the work of a Creator.”

Why? What makes you think that is the case?

Not quite, I agree that Owen’s argument was quite wrong, but his general thesis was correct and continues to be correct to today.

Now, does this mean that you finally accept that Owen’s theory involves a saltational process includes separate creation of animal groups?

It’s the predictions of common descent that we observe. That’s the problem.

HGT is not common design. It is inheritance.

Then you need to read up on ERV’s. If you are claiming that 80% of ERV’s inhibit retroviral infections through the transcription of complementary RNA then you are flat out wrong. Only about 10% of ERV’s have the sequences that could possibly do this. 90% of ERV’s are just LTR’s that do not inhibit retroviral infections.

Read what I wrote, then read the paper:

That’s transactivation, or activation in trans. This means the HERV-K insertion could be anywhere in the genome and still work in the same fashion. Anywhere. Now, what did I say before?

Who’s right?

This does nothing to explain why we see a nested hierarchy. You can use the same genetic mechanisms and not have a nested hierarchy. In fact, that is exactly how humans design organisms. We regularly take exact copies of genes and put them in very distantly related organisms.

That’s not what we see in nature. We see lineage specific solutions to different problems. For example, the vertebrate and cephalopod eye are different solutions to a camera type eye. Bats and birds have different solutions for flight. Nearly the entire mammal population of Australia demonstrates how different solutions exist for different habitats.

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I have not read any of the comments above. I am commenting here to express my general support for the existence of this thread because the Argument Clinic is my favorite Monty Python skit. Perhaps that is already obvious though, since I’m a commenter on this forum. Carry on.

None of your conclusions follow from your premises. Also, since most species that have ever lived are extinct, your supposed prediction is falsified.

That example falsifies your theory. The creator of ichneumon parasitism is not omnibenevolent.

Word salad. The genetic code is not a blueprint. It’s not a wave function. And it’s not an archetype. What Gould says doesn’t support any point you may be trying to make.

When you quote, you need to specify the source. “The article I gave you before” is not a proper citation. Sorry, but a gap doesn’t imply separate creation. Saltation creates a gap, because it involves instant change, as in the examples Owen provided in his publication you quoted from.

No, the code is in fact slightly different in various taxa. In fact your own cells contain two different codes. And that has nothing at all to do with “It seems that way but it is not that way”. Nor does it have anything to do with whether the history of life would be repeated.

Doesn’t that contradict your claim that the history of life would repeat?

That’s a very bad statement of what purifying selection is. Nor does this seem to be making any sort of point for you, much less anything relevant to what you were previously claiming.

In what way is that an example?

Note that none of your references have anything to do with common design. Nor do any of them have anything to do with nested hierarchy other than the last one, and it relies for its mechanism on there being an underlying phylogeny as well as the frequent horizontal transfer that happens in bacteria, not eukaryotes. Again, your sources do not support your claims.

I’m sorry, but your explanation was incoherent, so I can’t determine how to test for whatever it was.

Once again you completely misunderstand your source, which I doubt you have actually read. And in fact the little bit you quote doesn’t say what you claim it says. Don’t you get tired of this?

It means no such thing. Nor does your next reference, which I also strongly doubt you have actually read, have anything to do with your point. I’m getting tired of your inability to discuss anything.

No. Saltation and separate creation are antithetical. What do you think “saltation” means?

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