I see no denial.
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C. Parins-Fukuchi, G.W. Stull, S.A. Smith, Phylogenomic conflict coincides with rapid morphological innovation. Proc. Natl Acad. Sci. U. S. A. 118 (2021).
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DĂĄvalos, L.M., Cirranello, A.L., Geisler, J.H. and Simmons, N.B. (2012), Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biological Reviews, 87: 991-1024.
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C. Parins-Fukuchi, G.W. Stull, S.A. Smith, Phylogenomic conflict coincides with rapid morphological innovation. Proc. Natl Acad. Sci. U. S. A. 118 (2021).
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DĂĄvalos, L.M., Cirranello, A.L., Geisler, J.H. and Simmons, N.B. (2012), Understanding phylogenetic incongruence: lessons from phyllostomid bats. Biological Reviews, 87: 991-1024.
Have you read them?
I scanned (not an expert) the papers you provided. I saw nothing that indicated these conflicts, which exist across the entire tree of life not just the vertebrates, are predicted but they have been observed and noted. Both papers provided explanations for why the conflicts exist and as is the usual case suggest additional work that is needed to flesh out that explanation (Something almost every scientific paper seems to do. Teeing up future grant requests I guess). The papers also mention this supports micro and macro evolution. Something I am sure you wouldnât agree with.
My guess is no. He wanted to try to establish a problem but failed to note the papers provided a resolution to the problem. And even if he had read them he would just dismiss the work.
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I doubt there is. A quick scan suggests that
(i) neither paper says anything about the conflicts being âconcentrated at deep vertebrate nodesâ, though they do say they happen during radiations, and
(ii) this is in line with expectations of common descent, which doesnât predict perfect congruence because of known mechanisms (e.g. incomplete gene lineage sorting).
Agreed. Lets see if he confirms or denies reading them (The lack of links suggests he hasnât).
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Not the differences I was talking about. Given the 200k+ identical ERV insertions why do humans have <100 that are human specific and chimps have < 300 that are chimp specific. Also, for those insertions that match the mutations are the same. Sure looks and smells like a copying process.
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I read âPhylogenomic conflict coincides with rapid morphological innovationâ, but the other one I relied on secondary sources to give me general insights since it was a bit too technical for me.
I did not ask whether common descent can accommodate these observations but predict them. There is a difference.
Here is a snippet of the article I mentioned in the op-ed that briefly explains the similarties as well:
In the mid-19th century, Richard Owen and Charles Darwin proposed contrasting explanations for biological diversity. Owen argued that recurrent structural motifs across vertebrates reflect underlying generative laws rather than purely genealogical inheritance [1,2]. Darwin, by contrast, emphasized historical processesânamely, common descent and natural selection [2, 3]. Owenâs concept of a common archetype presents a fundamental structural blueprint that can be adaptively modified while retaining a shared organizational logic.
While Darwin attributed biological complexity to natural selection acting on random variation [2,3], Owen sought a deeper explanatory framework to account for the unity of structure observed across vertebrate forms. Owen argued that vertebrae are homotypic owing to a âvegetative repetition of a single vertebral elementâ [1]. These serially repetitive elements can then be teleologically modified, each acquiring distinct functions while preserving the underlying homology, often discernible only to trained observers. Notably, Owen acknowledged the limits of his knowledge. In the closing paragraph of On the Nature of Limbs, he notes, âTo what natural laws or secondary causes the succession and progression of such organic phenomena may have been committed we as yet are ignorantâ [1].
More than 150 years later, developments in molecular evolution, quantum biology, and viral genomics offer candidate mechanisms for the laws or secondary causes Owen anticipated. For example, the convergent co-option of endogenous retroviral genes, which are repurposed independently across multiple mammalian orders [4,5], parallels Owenâs notion of the âvegetative repetition of a single vertebral elementâ [1], in which a conserved structural module can be repeatedly adapted for new functions. Similarly, modular recombination and horizontal gene transfer can be interpreted not as mere accidents but as adaptive mechanisms operating within structural constraints, enabling viruses and host genomes to respond flexibly to environmental pressures [6,7].
Other researchers have recognized this pattern [8,9]: Gilbert [9], for instance, emphasized the deep molecular unity shared across all organisms, arguing that such universality reflects an underlying organizational plan consistent with Owenâs structural framework. The conceptual continuity between Owenâs archetype and modern modular genetic systems motivates a deeper structuralist reinterpretation. [emphasis added]
So you have no idea whether the source you cited actually says what you claim it does - as usual - and you didnât cite your actual source - as usual.
NCSE - Do Different Genes Mean Different Phylogenetic Trees?
Phylogenetic trees reconstructed from different genes in the same organism can differ. The possible causes of such differences are understood, ranging from methodological issues (such as different parameters being applied to the algorithms used to weigh sequence similarities) to bona fide biological phenomena. The latter are more interesting and significant, and are generally due to the effects of recognized evolutionary processes on the history of individual genes: convergence, the same sequence change appearing independently in different lineages either because of similar selective pressures, or by chance; changes in evolutionary rates , certain organisms evolve faster than others; horizontal gene transfer, sequences being transferred from one species to another by mechanisms other than vertical, linear descent; and timing, two lineages radiate from a third in relatively close succession, before enough differences may have accumulated between them to be able to discern the order of emergence. Thus, even in the best scenarios, absolutely congruent phylogenies from the analysis of individual genes are not expected.
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Which is why incongruities happen during radiations, and why minor incongruities (but not major ones) actually are predicted by evolutionary biology.
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I did not ask whether common descent can accommodate these observations but predict them. There is a difference.
You misunderstood what I meant. I was not suggesting that I did not read the source at all. Just not the entire article. I still read the abstract and the conclusion, which confirmed the claim that these conflicts happen at the family level as well rather than only the order level as the other study indicated.
The papers didnât provide a direct prediction in so many words that I remember but only an explanation. I assume the prediction was already known otherwise why provide an explanation.
On looking back at the papers I see the following which to me indicates the âproblemâ was predicted and/or known in advance.
Can you provide a link to any ID paper that predicts this and provides an explanation?
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Hybridization, horizontal gene transfer, and incomplete lineage sorting, rapid evolution and stasis, are all concepts that have been a part of population genetics for some time, and that trees will vary depending on the selection of particular markers are inherent in these very concepts. The central prediction that molecular phylogenies will largely conform to morphological phylogenies enjoys ample confimation, and this includes those constructed with arbitrary markers which are either not functional or not required to be identical to function.
While prediction and tests for falsification are powerful and essential validations of scientific understanding, I think much progress is also measured by explanatory power in resolving observations with the consilience of established broader knowledge.
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âHurry Up and Waitâ Pattern in the Fossil Record Supports Creation Model - Reasons to Believe
Gene-Tree Conflicts Make a Case for Creation - Reasons to Believe
Here are snippets from the op-ed article as well:
Owenâs interpretation of biological organization was shaped by the empirical taxonomic debates of his time. Georges Cuvier rejected the Great Chain of Being in favor of embranchments, referring to distinct anatomical groupings not arranged along a single linear continuum [9]. Owen adopted this branching view but overlaid his theory of archetypes onto it, using both to explain discontinuities in the fossil record and structural gaps between major groups [9]. In Owenâs formulation, each embranchmentâvertebrates, mollusks, arthropodsâpossesses its own archetype, expressing a characteristic pattern that constrains but does not rigidly determine the forms within it. Owen argued that the realized forms in naturerepresent only a subset of what the archetype could, in principle, generate [1].This idea of the successive introduction of specific formsechoes a pattern of emergence rather than strict lineage. It anticipatesânot mechanistically but conceptuallyâan evolutionary logic driven by structural potential rather than descent alone.
Owenâs developmental perspective:
Richard Owen proposed that biological form is governed by underlying structural laws, and that major morphological differences can arise through reorganization or interruption of developmental processes. In this view, the emergence of distinct structural âtypesâ is not necessarily continuous but may involve discrete transitions corresponding to higher taxonomic divisions, such as families or orders [1].
- R. Owen, On parthenogenesis, or the successive production of procreating individuals from a single ovum (John Van Voorst, London, 1849).
9.S. F. Gilbert, Owenâs vertebral archetype and evolutionary genetics-A platonic appreciation. Perspect. Biol. Med. 23(3), 475â88 (1980).
Yeah but, I am talking about specifically at the family and order level, which was what my question was directed towards. Does common descent predict it at those levels specifically?
So, since conflicts happen at different taxonomic levels, there is no âconcentration of such conflicts at deep nodesâ, and if archetype theory predicts that, itâs refuted.
(and your source doesnât match your claim, as usual).
The first is about stasis, and doesnât mention phylogenetic/phylogenomic conflict at all.
Itâs yet another cite that doesnât match his claim, that he probably hasnât read.