I specifically asked consistently about conflicts at deep vertebrate nodes not deep nodes in general. Moreover, the source in question specifically said in the abstract:
“For more than a decade, evolutionary relationships among members of the New World bat family Phyllostomidae inferred from morphological and molecular data have been in conflict.”
Families along with Orders are what we would expect to find conflicts.
I mentioned that source in conjunction with the other source to show more evidence of how their model predicted in advance what we found later in the genetic level.
So you are talking about “specifically at the family and order level”, while they are showing conflicts between genera within a single family.
Your source doesn’t match your claim, as usual.
But it didn’t show that, because it’s about stasis, not about conflicts. Morphological vs genetic doesn’t make any difference.
Your source doesn’t match your claim, as usual.
How many times do you need to catch some-one misrepresenting sources that they haven’t understood and probably haven’t even read, before it can be assumed that any source they cite is likely to misrepresented, misunderstood and unread?
And my point is that no one has offered any other coherent framework to interpret them.
So use the fact that HGT occurs to explain the data we have on ERVs. Vague assertions are of no use in science – start talking about data.
Which has what to do with the value of ERVs as evidence for common descent?
Which has what to do with the value of ERVs as evidence for common descent?
Common descent, as understood by contemporary evolutionary theory, includes reticulation, modularity, and the role of constraints in evolution. So what does this have to do with the value of ERVs as evidence for common descent?
Clearly you think that, but nothing you have presented here support that belief.
Really? Please explain how Owen’s theory explains the correlation between the degree of divergence with ERV families and the species range within which the family is found?
Sorry, but quantum biology provides no hint at all for a candidate mechanism.
Yeah my bad on this one. I misunderstood that part of the study.
Yes, I knew that already about the study. But, this isn’t the reason why I decided to include it with the other article. I think you probably should have asked me why I believe it was more evidence for the claim rather than jump the gun here.
Before I more directly address your comments, I want to mention something that might help understand my point better. I argued that the existence of ERV’s contradict common descent because observations strongly suggest that viruses were the first life forms that were used as building blocks to create all the other life forms. If the virus-first hypothesis is not true, then I think ERV’s could fit the current common descent framework.
G. P. Fournier, et al., Ancient horizontal gene transfer and the last common ancestors. BMC Evol. Biol. 15, 70 (2015).
J. Simpson, C. A. Kozak, G. Boso, Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLOS Genet 18, e1010458 (2022)
I had to copy and paste this from AI because the original article was under a paywall:
Key Reasons for Exclusion (Summarized from the 10 points)
No Universal Genes: Unlike cellular life, which shares a common set of genes (e.g., ribosomal proteins), no single gene is shared by all viruses, making a unified phylogeny impossible.
Polyphyletic Origins: Viruses are not a single, ancient lineage but rather a collection of multiple, independent, and recent origins derived from host cells (polyphyly).
Horizontal Gene Transfer (HGT): Viral genomes are highly unstable and largely composed of genes stolen from hosts via HGT, rather than being “inventors” of new, fundamental genes.
Inability to Self-Sustain: Viruses are inert outside a host; they lack metabolism and machinery for energy production and translation, requiring host cells for replication.
“Virocell” Concept: The authors suggest that the true, functional, metabolic entity is the infected cell (virocell), while the virion is merely a “packet” of genetic material.
Molecular Parasitism: Their origin is likely due to the continuous escape of genetic material from cells, not an independent, ancient branch of life.
Conclusion
Moreira and López-García conclude that viruses are not part of the tree of life (which tracks organismal phylogeny) but are instead essential, highly mobile agents that facilitate horizontal gene transfer across the “roots and stem” of the tree of cellular life.
Here is another snippet of the article regarding this…………………
Owen’s account was framed within Christian–Platonic assumptions and a providential reading of nature [34,16]. Our proposal generalizes this structural logic into a fully naturalistic, quantum-informed model in which the first living systems emerge in deep, energy-rich marine environments that we take to be conceptually reminiscent of the primordial waters motifin Genesis 1, rather than Darwin’s “warm little pond” or Hameroff’s proto-conscious objective reduction (OR) scenario [35]. This raises the question of whether the earliest stages of prebiotic chemistry exhibit constraint-driven behavior analogous to Owen’s archetypal ordering.
2.4.1 A Coherence-Biased, Field-Guided Origin
In a hydrothermal-vent scenario, in which life emerges within thermodynamically open, energy-exchanging environments capable of sustaining transient quantum coherence, coherent domains could stabilize reaction pathways, biasing polymer formation and template replication without invoking any external purposive agency [10]. Minimal circular RNAs and ribozymes could arise abiotically on vesicle surfaces and mineral interfaces where π–π stacking, weak electromagnetic fields, structured water layers, and quantum electrodynamics–like ordering promote organized assembly. These environments provide a physically tractable mechanism forearly polymer stabilization, analogous to a quantum-annealing bias toward low-free-energy configurations (see Appendix).The potential roles of horizontal regulatory transfer, vesicle–vesicle interactions, and coherence-modulated template dynamics may be important early drivers of chemical innovation. Structural analogues are summarized in Table 1. Importantly, this framework does not rely on OR, proto-feelings, or other nontestable teleological constructs.
2.4.2 Integration of the Virus-First Perspective
The virus-first hypothesis, originally articulated byEugeneKoonin and William Martin and refined in more recent models [36], proposes that precellular, virus-like ribonucleoprotein systems may have presented the earliest replicators. These entities would have emerged in dynamic, energy-rich settings characterized by rapid turnover, modular recombination, and encapsulation. Although debated relative to RNA-first models, the virus-first scenario aligns with the coherence-biased origin proposed here: Both posit that early replication occurred in open, far-from-equilibrium systems lacking complex cellular machinery.Where virus-first emphasizes genetic modularity, our framework emphasizes the physical substrate that could render modular precellular replicators chemically viable; this substrate consists of structured surfaces, coherence domains, and field-stabilized templating. In this sense, coherence-stabilized polymers may represent a precursor stage to the modular ribonucleoprotein replicators envisioned in virus-first models.
I’m not denying that ERV divergence patterns correlate well with common ancestry models. Clearly they do, and that is one reason ERVs are often considered strong evidence for descent relationships.
My point is different.
Owen’s framework was never a genomic theory in the modern sense, since he predated genetics entirely. The argument is not that Owen himself explained ERV families specifically, but that structural/archetypal interpretations of biological organization existed before Darwin reinterpreted homologous similarities primarily through common descent.
As discussed in the article, both Owen and Darwin recognized nested biological patterns, but they interpreted them differently. Darwin explained them historically through descent with modification, whereas Owen interpreted them as expressions of deeper structural laws acting through conserved archetypal constraints alongside adaptive variation.
What makes this relevant today is that modern evolutionary biology itself has increasingly moved beyond a strictly simple branching “Tree of Life” model. Horizontal gene transfer, reticulate evolution, viral integration, convergent co-option, and network-like genomic interactions complicate purely vertical inheritance models.
So the real question is not whether ERV patterns fit a modern framework of common ancestry — they clearly do now. The question is whether they uniquely necessitate common ancestry to the exclusion of every alternative structural or constraint-based interpretation.
For example:
are ERV integrations entirely random,
are there insertional biases or conserved genomic hotspots,
and could some shared patterns reflect deeper organizational constraints or modular reuse rather than only historical descent?
That does not mean common ancestry is false. It means the inference from “shared ERV structures” to “therefore only common descent can explain this” may go beyond what the evidence itself strictly establishes.
I beg to differ. I think quantum biology does provide at least plausible candidate mechanisms relevant to biological regulation and informational stability, even if those mechanisms do not yet directly explain macroevolutionary change.
For example, the article discusses DNA-mediated charge transport (CT), a well-studied quantum-mechanical process involved in genome surveillance and repair.
Research by Tse et al. demonstrated that DNA repair proteins containing [4Fe–4S] clusters use charge transport through π-stacked DNA to detect lesions across thousands of base pairs. When DNA stacking remains intact, electron transport proceeds efficiently; when mismatches or structural disruptions occur, charge transport is interrupted, helping localize repair activity.
What makes this important is that the mechanism is sensitive to the physical organization of DNA itself. Well-ordered nucleotide stacking supports efficient long-range signaling, whereas disordered regions disrupt transport and correlate with increased mutational vulnerability.
That does not prove some grand quantum-archetype theory. But it does provide a concrete example where quantum-mechanical effects influence biological regulation, stability, and error correction in a nontrivial way.
So when people say quantum biology offers “no hint at all” toward possible mechanisms, I think that overstates the case. At minimum, processes like DNA charge transport show that biological systems can exploit coherence-sensitive quantum effects in functionally meaningful ways.
The broader question is how far such mechanisms extend and whether they scale beyond local molecular regulation into larger evolutionary or organizational dynamics. That remains debated, but it is not accurate to say there are no candidate mechanisms whatsoever.
actions of a super-intelligent, supernatural Mind = “God did it”
Saying something is supernatural means it is untestable. It can not challenge an established scientific theory. You can chose to believe it but don’t expect to successfully challenge the established science.
And since you are so big on predictions, neither of the articles you provided actually predicted the issue you are trying to use to beat evolution on the head. Care to try again? I wanted to see a source that predicted the problem and then showed how ID addresses the problem.
And no comment on the actual nature of the Gilbert paper and his reference?
Not necessarily. It all depends on how define supernatural.
One reason many people think God cannot even be considered within a scientific framework is because they assume only two options exist: materialism or substance dualism. But there’s a third alternative that often gets overlooked: idealism, or more broadly, information-based metaphysics.
Very briefly:
Materialism: matter is fundamental, and mind emerges from matter.
Substance dualism: mind and matter are two separate fundamental substances.
Idealism/informational realism: informational or mind-like structure is fundamental, and what we call matter emerges from deeper informational relations.
I’m not arguing for substance dualism or for a separate supernatural “realm.” I’m arguing for a single underlying reality in which physical systems may emerge from a deeper informational structure.
From that perspective, space-time itself may not be fundamental. Some approaches in modern physics already explore this possibility, where spacetime emerges from deeper quantum or informational relationships. If time is emergent rather than ultimate, then questions like “what happened before time?” or “how do you create time?” may be category errors, because creation would not occur within time but would instead refer to the grounding of time itself.
So the question becomes less:
“How do you create something that always existed?”
and more:
“What explains the existence and structure of time and physical law in the first place?”
That’s where the Logos concept becomes relevant to me.
In John 1, the Logos is described as the rational principle through which reality is structured. The Greek term logos carries meanings closer to reason, intelligibility, structure, and ordering principle—not merely “spoken word” in the modern sense.
So my argument is not that God is a magical physical object inserted into the universe from outside nature. My argument is that reality may itself be grounded in a deeper rational or informational structure from which physical systems emerge.
That idea is not completely disconnected from modern scientific thought. There are already serious discussions in:
information-theoretic approaches to physics
quantum foundations
emergent spacetime models
mathematical/informational interpretations of reality
None of that proves Christianity. I’m not claiming it does. My point is narrower: once reality is viewed as fundamentally informational or mind-compatible rather than purely material, a Logos-based metaphysical interpretation becomes philosophically possible in a way that strict materialism tends to rule out from the beginning.
I thought that was what the article suggested here. You just have to click the blue link to see how their model predicted these results. Unless I am misunderstanding what you are asking for; In that case, please provide an illustration of what you want instead………………
In scientific research, conflicts between different data sets and sets of measurements, or between observations and theoretical explanations for the observations typically are strong indications that the scientific model undergirding the measurements, observations, and theoretical explanations is either incorrect or in need of major revision. Nearly two years ago, I wrote an article, New Speciation Model Challenges Evolution, Supports Creation, in which I showed that major mismatches exist between phylogenetic trees (evolutionary history based on genetics) and paleontological trees (what the fossil record shows). These inconsistencies present a major challenge to deistic and nontheistic evolution models for the history of Earth’s life and, alternately, strong evidence for a biblical creation interpretation.
Now, a team of three computational evolutionary biologists has written a paper examining the biological significance of the many examples of phylogenetic conflicts and rapid morphological (having to do with form, structure) innovations that biologists and paleontologists have observed in the history of Earth’s life.1 Specifically, they demonstrated that “instances of high gene-tree conflict (discordance in phylogenetic signal across genes) in mammals, birds, and several major plant clades correspond to rate increases in morphological innovation.”2
I think you are free to speculate that the fundamental forces are tuned to present necessary and sufficient conditions to allow for life generally, but a common quantum mechanism that then directs speciation, acting on one branch to be carnivorous predators and another to be plant eating prey, could never drive macroevolutionary change. The reason is ecologies are populated by distinct and varied organisms, but quantum processes, once the basic properties are defined, are all exactly identical and interchangeable. There are no predator or prey leaning quantum processes. New rules must emerge and that is what evolutionary theory provides.
I think you may be misunderstanding the type of claim being proposed.
The framework is not suggesting that quantum processes directly encode “predator” or “prey” identities, nor that quantum coherence somehow persists across organismal or macroevolutionary timescales.
The proposal is much narrower and more structural.
At the molecular level, transient quantum effects — such as tunneling probabilities, charge transport efficiency, or conformational biases — may subtly influence biochemical stabilization under non-equilibrium conditions. These effects are short-lived and localized, entirely compatible with established decoherence limits.
The key idea is hierarchical constraint propagation across nested biological scales:
molecular → regulatory → developmental → evolutionary.
In this framework:
transient molecular biases can become stabilized within gene regulatory networks,
and developmental constraints shape the morphospace within which natural selection operates.
So the proposal is not that quantum mechanics replaces ecology, selection, developmental biology, or evolutionary dynamics. It is that lower-level physical constraints may help structure the landscape within which those higher-level processes unfold.
I actually agree with you that higher-order rules and emergent ecological dynamics are necessary. The disagreement is whether biological evolution operates over a largely unconstrained combinatorial landscape, or whether deeper physical and informational constraints significantly bias which forms become stable, repeatable, and evolutionarily accessible.
In other words, quantum-informed approaches here function more as boundary-condition modifiers and constraint-shaping influences than as direct species-level “drivers” of predator/prey roles.
The ‘virus-first’ hypothesis is a confusing name because the definition of a virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism.
I understand that it is not your fault that other people have invented such an oxymoron name for the hypothesis. Precellular replicators may be an acceptable hypothesis (speculation) if we think that the precellular replicators had a replication mechanism in addition to the hereditary code and a wall that kept the stuff together. The precellular replicators needed to be quite cell-like to work.
I don’t see a prediction in the Ross articles. Ross just points out a known issue and then plays the “God did it” card to explain it. Which is the typical ID/YEC methodology. Just because there is a not yet answered objection to a theory doesn’t make the theory invalid. We just don’t know yet. Look at all of the original objections to Darwin’s theory and how they were answered over time.
And there you go off into another AI generated rabbit hole. We’re talking about science. You know the study of reality. Trying to bring in God makes it metaphysics.
PS: It is usually quite easy to identify AI generated text. I wonder how anyone gets away with it for school work. I asked ChatGPT and it provided 8 clues to identifying AI generated text.
Yes, this is precisely why I think the existence of ERV’s contradict common descent because this is only the case for a Darwinian framework NOT Owen’s framework. As I mentioned before, observations strongly suggest that viruses were the first life forms that were used as building blocks to create all the other life forms. However, If the virus-first hypothesis is not true, then I think ERV’s could fit the current common descent framework. Here are snippets of the article explaining the differences between the two theories and the mechanism used to produce these precellular viruses. Of course, you can just skip the reading if you fully understand my point now:
Darwin and Owen framed the origin of life in fundamentally different ways. Darwin, who never published a formal theory of abiogenesis or the origin of life, speculated that life might have arisen from undirected chemical reactions in a “warm little pond,” anticipating later naturalistic models of prebiotic evolution [33]. For Owen, biological form precedes matter: Life begins when this archetypal structure is impressed upon germinal material, which would mark the first instantiation of an underlying structural blueprint, with diversification occurring as periodic re-expressions or constrained deviations from this generative scheme. This distinction between contingent chemical emergence (Darwin) and law-governed structural initiation (Owen) remains central to debates in structuralist and evolutionary theories…………….
Chemical Foundations of Life
Scientifically, this period corresponds to a world dominated by non-equilibrium chemical systems. Reactions likely occurred in settings like hydrothermal vents beneath the ocean, mineral-water interfaces on early seafloors, or ice grains and clay surfaces, which can concentrate and organize simple molecules. These environments enabled molecules to interact non-randomly and repeatedly—conditions now considered crucial for the emergence of early biochemical order [7, 8, 9, 10].
One leading model suggests that life began in alkaline hydrothermal vents, where naturally forming compartments (or vesicles) emerged from simple, fat-like molecules. These vesicles helped gather and concentrate chemical building blocks, allowing primitive cycles of chemical reactions to begin [11].
Note on Speculation: Quantum Coherence in Prebiotic Chemistry
We propose that these environments might have allowed short-lived quantum coherence—a state in which particles like electrons or protons behave in a coordinated way. In this view, coherent dynamics may have biased the formation of polymers (like RNA). These effects could have favored template-based replication, helping early chemical systems to “search” for stable, low-energy configurations [12, 13]—an idea loosely comparable to quantum annealing.
This idea is speculative and does not imply “quantum consciousness” or intentional design. It is one possible way to explain how physical constraints may have nudged early chemistry toward order rather than randomness.
Modern biology offers clues about these early processes. For example, circular RNAs and self-cleaving ribozymes are found across diverse organisms. These minimal RNA replicators are chemically robust and could plausibly have arisen on vesicle surfaces or mineral substrates under early Earth conditions [14, 15]. On early Earth, they may have formed on mineral surfaces or inside vesicles, guided by weak forces like π–π stacking and structured water layers [12, 13].
Such features suggest that early chemical evolution was not purely random. Instead, it may have followed biased, constraint-driven pathways that favored the emergence of information-bearing molecules like RNA viruses [7, 8, 9, 12, 16].
Well first off, I did get a chance to read the article in question even though it is behind a paywall. Second, I was not referencing that particular article as a data point. It was the first two articles that were being used as data points.
The inference of branching common ancestry arising from ERV mapping is based on understanding of viral infection of germ lines and population genetics. This is remote from OoL, even if there were replication in a pre-cellular world.
In other words, the naturalistic biological evolution model based on phylogenetics predicts that introduction of new species has exceeded extinctions, but the fossil record shows that the reverse is true. The research team did not address the fact that the discrepancies between phylogenetics and the fossil record appear to increase with the complexity and the adult body size of the genus. By contrast, such a correlation is predicted from a biblical creation model perspective for life.
Such as what?
This begs the question again.
How are you defining God?
As I mentioned earlier, I use AI at times to edit my own responses in a way that is more concise, clear, and addresses the point. I was honest and upfront about this before. But, it is not completely generated unless I mention it, which I have.in the past.
I did already in the op-ed.
The framework is not proposing a single rigid “blueprint” for all life in the sense of a fully predetermined biological schematic. Rather, it proposes a structured space of possible forms governed by generative constraints. In Owen’s language, the archetype functions more like a flexible organizational principle than a literal template for every organism.
So the idea is not that there is one static blueprint that periodically gets rewritten, but that biological systems explore a constrained morphospace in which certain structural configurations are more stable, accessible, or information-efficient than others. Changes in biological form emerge as systems move through this constrained solution space under developmental, energetic, informational, and potentially quantum-level constraints.
Here is a snippet of the article that addresses this in more detail:
Owen’s theory of archetypes, especially his notion of a universal common archetype, emerged from the intellectual milieu of German Naturphilosophie(ca. 1790–1830), where anatomical patterns were interpreted as manifestations of underlying lawlike principles rather than historical accidents [16]. Although his framing was shaped by Christian–Platonic commitments, the structural logic of the archetype can be analyzed independently of such assumptions. In this paper, we retain his core insight—that recurrent patterns in biological form reflect genuine constraints—but reinterpret those constraints in physical and informational terms. Rather than suggest divine intention, we examine whether nonstochastic, possibly quantum-informed mechanisms constrain the morphospace accessible to evolving systems.
Owen’s universal common archetype proposes that fundamental biological forms—types—are governed by generative laws that constrain how structure emerges. He viewed the archetype as a flexible yet bounded template, organizing serial elements into topological patterns repeated across taxa [1,8]. He further suggested that only a portion of this full configurational space has been realized on earth and speculated that its organizing principles might extend to life in other worlds, provided the same universal constraints apply [1].
Conceptually, this notion could be considered loosely analogous to the universal wave function in quantum mechanics, particularly in many worlds–type interpretations (see Table 3). In quantum theory, the universal wave function evolves deterministically according to the Schrödinger equation and encodes all possible configurations of matter and energy. We do not claim equivalence between Owen’s archetype and the wave function. Instead, we use the analogy as a heuristic: Both concepts describe a structured space of possibilities (see Appendix).Empirically, large-scale cosmic structures exhibit fractal and network-like topologies statistically similar to those observed in biological and neural systems [17,18]. Such patterns are shaped by geometric and energetic constraints that promote scale-free, hierarchical organization across physical, biological, and cognitive domains [19]. In Owen’s terms, these constraints can be viewed as the “laws of form” that bias systems toward particular structural basins.
In our framework, these multilevel constraints, subsequently expanded to include informational, thermodynamic, and quantum-search restrictions, collectively frame biological evolution as occurring within a narrowed solution space (summarized in Table 1). We build on this structural logic by examining whether quantum-coherent regimes and collapse-like transitions—operating through coherence, tunneling, decoherence, and hypothesized collapse threshold behaviors (see Table 2 and Appendix)—can heuristically serve as deeper physical analogues of the archetypal limits Owen envisaged. Figure 1 provides a schematic overview of these relationships, including the treatment of entanglement as a correlational property that may be present within multiple dynamical regimes rather than as an independent constraint level or causal mechanism.
As I mentioned before and the article suggests, the framework does not treat germinal material as existing entirely independently of organization or constraint (i.e. substance dualism). Rather, the proposal is that the constraints and the material system co-exist as part of the same physical process (i.e. Idealism). In other words, the archetype is not an externally imposed schematic floating apart from biology, but a description of the lawful structural tendencies that shape how biological organization emerges in the first place.
This is why the paper compares Owen’s archetype heuristically—not equivalently—to concepts like the universal wave function: both describe structured spaces of possibility rather than fixed blueprints specifying every final outcome in advance.
