At a minimum, there needs to be analysis of real world data which is completely missing from the paper for the claims you are trying to make. For example, there is absolutely no tie between stuff like quantum effects in microtubules and the observed spectrum of mutations in a genome. The concepts are all disjointed without anything really connecting them, and the claim about these concepts are dubious at best.
I am looking for small excerpts, not entire sections where the answer may or may not be located. You have pointed to large sections of the paper claiming the answer is in there, but I have yet to find the answers in these sections of the paper.
Itâs the case for the vast majority of biologists. You are going to have to do a LOT of heavy lifting to justify the causal role for function, none of which is found in the paper. All you seem to be saying is âbecause ENCODE says soâ. Thatâs not going to work.
None of which is supported by data with respect to mutations and genetics.
You are going to need a LOT of data to back up that claim, none of which is in the paper.
Papers are not recommendations. If you are going to make these claims then you are going to need these analyses.
No, they arenât. You can mix and match coding modules in violation of a nested hierarchy.
The data you are citing is based on just existing, no necessity evidenced.
I have already responded to this. Microtubules are not the biological mechanism of Owenâs extended theory itself, but rather the site or medium where quantum processes take place.
Quantum tunneling is an important phenomenon that occurs in both microtubules and during the process of mutations.
So, they are not directly related processes, but I referenced those studies to illustrate how quantum tunneling plays a role in both microtubules and mutations. Furthermore, I provided studies that highlight how quantum tunneling and coherence is a precise non-random or self-organizing process, such as Patelâs suggestion that the genetic codeâs structure mirrors quantum algorithms, allowing efficient, error-tolerant protein synthesis. This may imply that natural selection or law capitalized on DNAâs quantum properties for precise replication.
Further research reveals biological systems, like electron transfer in energy production, exhibit quantum tunneling similar to engineered devices, showing optimization beyond classical theory. These insights bridge quantum mechanics and biological processes, underscoring a sophisticated natural design in biological functions:
A. Patel, Quantum algorithms and the genetic code. Pramana J. Phys. 56, 367â381 (2001).
C.C. Page, C.C. Moser, X. Chen, P.L. Dutton, Natural engineering principles of electron tunnelling in biological oxidationâreduction. Nature 402, 47â52 (1999).
In order to adequately address your questions, you have to read the full context of what I am arguing or else you will end up asking the same question or not be convinced that I answered your questions at all. .
For example, you accused me of putting the cart in front of the horse when you quote mind what I said here: âAerts and ArguĂ«lles (2022) demonstrated that quantum theory could model cognitive processes such as decision-making,â
If you read the whole section or context, you probably would not have done this.
You are missing the point. We are not here trying to justify the causal role definition of function. Instead, we are justifying why a conscious agent is evident and detected by science. This is why it is not found in the paper. Moreover, we do provide more ways to test and confirm whether this argument is supported or not.
For example, if evidence confirms a correlation between microtubule vibrations and viral activity, influenced by quantum processes, it will imply a direct link between quantum phenomena and physiological functions. Viruses, as fundamental structural blueprints, facilitate interaction with host cells through convergent co-option and HGT.
To test this, researchers could investigate microtubule dynamics during viral infection using techniques like atomic force microscopy. Statistical analyses would assess correlations between microtubule changes and viral replication rates. Experiments manipulating microtubule dynamics would determine causality. This evidence would challenge the traditional view of endogenous retroviruses (ERVs) as non-functional remnants, suggesting a functional or causal role in evolution, contrary to Darwinian evolutionâs implications.
The paper provides substantial evidence suggesting that constants, such as the fine-structure and cosmological constants, are finely tuned and play essential roles in the universeâs structure and evolution. These constants, as illustrated, facilitate atomic and biochemical stability, influence evolution, and contribute to life-compatible environments through quantum processes, such as electron tunneling. The cosmological constantâs precision supports cosmic stability and the formation of habitable systems, and deviations could imply physics beyond the Standard Model.
However, we have already acknowledged already that our research doesnât address broader questions in quantum physics, as these topics lie beyond the scope of our article. Although we do have a quantum gravity model, to validate it, testable predictions must be derived from a well-defined mathematical model of the cosmos.
Future research and upcoming experiments, such as the Euclid space telescope, NASAâs Wide-Field Infrared Survey Telescope (WFIRST), and the Simons Observatory currently under construction in Chile, hold promise in addressing these limitations. These missions aim to investigate whether the influence of dark energy was stronger or weaker in the past compared to the present.
Why? As we pointed out in our paper, Our methodology dismisses cladograms and phenograms as inconclusive evidence of evolutionary continuity. While these diagrams mimic the appearance of phylogenetic trees, they fall short in establishing genuine ancestor-descendant relationships within the data. Instead, we advocate for additional phylogenomic analysis to determine whether specific taxonomical groups should be classified separately and the gaps in the fossil record between these taxonomical groups are considered real, which diverges from evolutionary theory.
We provided sources that support our claimsâŠ
W.L. Hatleberg, V.F. Hinman, Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change in Current Topics in Developmental Biology (Vol. 141, Ch. 2, pp. 39â73), S.F. Gilbert, Ed. (Academic Press, 2021), 39â73.
G.S. Hornby, Modularity, reuse, and hierarchy: Measuring complexity by measuring structure and organization. Complexity 13, 50â61 (2007).
The ENCODE Project did much more than assign function to sequences based on its mere existence in the human genome. The ENCODE Project experimentally determined which sequences in the human genome displayed biochemical activity using assays that measured:
transcription,
binding of transcription factors to DNA,
histone binding to DNA,
DNA binding by modified histones,
DNA methylation, and
three-dimensional interactions between enhancer sequences and genes.
The implied assumption is that if a sequence is involved in any of these processesâall of which play well-established roles in gene regulationâthen the sequences must have functional utility.
So show how the data is consistent with your claims. Map the distribution of mutations and their effects and show how it is consistent with the mechanisms you are proposing.
Itâs a simple category error. All horses are mammals, but not all mammals are horses. Some quantum processes are involved in consciousness, not not all quantum processes are the product of consciousness.
You need to show a direct link between microtubules and controlling which mutations occur and which mutations are selected for.
In what way do they influence evolution?
Why do they not evidence common ancestry and evolutionary mechanisms?
Itâs rather obvious why gaps in the fossil record are not evidence. We donât expect that we have anything close to all of the species that ever lived in our fossil collections. We have only surveyed a tiny, tiny portion of Earth for fossils. I think it is laughable to pin the hopes of a theory on the idea that our fossil collections are complete, especially given the fact that new transitional fossils are found on a yearly basis.
How do they support your claims?
Biochemical activity is not the same as function.
Which is nonsense. You are ignoring the possibility that a sequence can have those functions and not be involved in regulating a gene. There is absolutely no reason to think that a transcription factor binding site necessarily must regulate a gene.
Slocombe L., Winokan M., Al-Khalili J., Sacchi M. (2023). Quantum tunneling effects in the guanine-thymine wobble misincorporation via tautomerism. J. Phys. Chem. Lett. 14, 9â15.
Thank you for illustrating my point before. You are now straw manning the argument.
Why? The main mechanisms we use in support for our theory is convergent co-option and HGT in regards to viruses. Non-random mutations is a very small part of the overall process compared to the other mechanisms. I think you are again shoehorning your model of species into ours when they both interpret the evidence very differently.
Moreover, since I made it clear to you before that Microtubules are not the biological mechanism of Owenâs extended theory itself, but rather the site or medium where quantum processes take place, the only thing I would need to show is that quantum processes, such as quantum tunneling, happen in mutations as well, which I have already provided .
The law of entropy exemplifies how these constants contribute to evolutionary mechanisms, such as mutations or natural selection, as it explains how evolution emerges with functional, self-organizational order through energy dispersal by gradient reduction, serving as the motive force behind hierarchical organization. This universal law transcends the boundary between animate and inanimate systems, as both evolve through energy flows toward stationary states relative to their surroundings
As you know, entropy impacts biochemical structures and genetic variation by driving the tendency of systems to increase in disorder, dispersing energy and leading to more stable, low-energy configurations.
Because there is an alternative explanation for them in the form Owenâs theory that does not require us to interpret them as ancestral relationships.
Which theory are you referring to here? Because it sounds like you are placing the burden of proof on us when our theory is much more parsonmiousnous since we are not making addtional claims that there are numorous other fossils out there that canât be found or werenât found yet. It is much easier to just accept that the gaps are real and move on.
They provide a possible reason why nested patterns were used to construct species.
I think the meds Iâm on after some minor surgery have me giddy; I couldnât stop laughing here.
Some explanation: in grad-school-prep philosophy courses we invented a Dutch philosopher and went to the effort of getting him listed â one Gerhardt DeHoors â in the library reference list of philosophers. This was all done in pursuit of a bad joke, that too many thinkers are guilty of putting Descartes before DeHoors.
Based on the titles and abstracts, the first seems to be about gene regulation in sea urchins, and the second about devising general metrics. Neither looks likely to support your claims regarding software engineering and nested hierarchies.
They probably donât, and that wasnât your claim.
What is convergent co-option, and what does it look like at the sequence level? How does it differentiate your theory from the theory of evolution?
The mutations that happen through these mechanisms are random with respect to fitness. They are not non-random.
Biology follows the same laws as everything else in the universe? This is your big piece of evidence? Those same laws govern weather and the Earths volcanism.
Entropy impacts all processes in the universe in the same way. I donât see what this has to do with anything.
Just as invisible pink gravity unicorns can be an alternate explanation for the orbit of planets. This doesnât change the fact that the orbits of planets are accurately predicted by General Relativity.
The theory of evolution predicts a nested hierarchy. We observe a nested hierarchy. No theory of design requires a nested hierarchy because a designer can mix and match parts in ways that violate a nested hierarchy. Your argument was already refuted 140 years ago.
In design, components are often reused in varied ways across different applications, as is seen with organisms sharing similar genetic structures based on a âcommon blueprint.â Convergent co-option in biology demonstrates this concept. An example can be seen in viruses, where genetic elements are reused in different organisms without implying common descent. This study illustrates how viral elements are co-opted across species without requiring evolutionary ancestry:
Simpson, J., Kozak, C. A., & Boso, G. (2022). Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLOS Genet, 18, e1010458.
Youâre correct according to a strict interpretation of ârandom with respect to fitness.â However, we utilize the causal-role definition of function and a definition of randomness consistent with Ayalaâs (2007) description: mutations are âunorientedâ regarding adaptation and occur without regard to benefit or harm to organisms.
Yes, and these laws, including entropy, are foundational in understanding adaptive processes across living and non-living systems. Owenâs extended theory posits that a âcommon archetypeâ reflects intentional design rather than descent from a common ancestor, as seen in the vertebral homology across vertebrate species. He proposed two causal mechanisms: a âpolarizing forceâ that organizes patterns during development and an âadaptive forceâ that responds to environmental pressures.
Entropy drives self-organizing processes by creating functional order through energy gradient reduction. This universal process applies to both biological and non-biological systems, with hierarchical organization arising as energy is distributed toward stable states. Our view of consciousness aligns with Aerts and Arguëlles (2022) and recent studies showing quantum-like behavior in cognitive processes, with Penrose proposing orchestrated quantum processing in microtubules as the basis of unified consciousness.
Indeed, both points are accurate and underscore our argument for Owenâs extended theory. Nested patterns, such as those influenced by viruses, can occur via convergent co-option and horizontal gene transfer (HGT). In synthetic biology, viruses are used to design organisms, paralleling patterns seen in nature. However, viruses also disrupt hierarchical patterns, such as RNA viruses, which cannot fit within the Tree of Life due to their lack of cellular characteristics and unique polyphyletic origins. Moreover, HGT complicates phylogenetic relationships by introducing genes from diverse sources into single genomes, supporting our argument that Owenâs theory better accounts for both nested patterns and their exceptions.
The study supports our claims by showing how our explanation is better than random noise. For instance, protein-protein interactions (PPIs) in crowded cellular environments are highly structured, enabling specific interactions while minimizing unwanted ones.
Robust proteinâprotein interactions in crowded cellular environments. PNAS.
A subsequent study by Harvard indicates that cellular concentrations of PPI-participating proteins are precisely regulated, underscoring the high specificity and precision needed for life. This observation aligns with Fuz Ranaâs point that these fine-tuned interactions suggest an underlying intentionality in biochemical systems.
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions. PNAS.
Since you didnât answer, the most likely scenario is that you havenât read the papers you cited (just as you have previously been caught doing),you have no idea whether or not they support your claims, you probably donât even what they are about, and your claims can be rejected with great force and abundant condemnation.
Sorry about that. Let me focus on doing that now. I read most of this article, which does support the claim that software engineering principles like easier maintenance, code reuse, and scalability are closely tied to the concept of nested hierarchy:
W.L. Hatleberg, V.F. Hinman, Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change in Current Topics in Developmental Biology (Vol. 141, Ch. 2, pp. 39â73), S.F. Gilbert, Ed. (Academic Press, 2021), 39â73.
Here is a snippet of the article:
Conclusions
Complex biological systems are both modular and hierarchical, and GRNs provide a mechanistic framework to understand evolutionary change. Research often examines concepts such as pleiotropy, co-option, modularity, and homology; however, it is impossible to fully understand these ideas without examining the entire hierarchical system. Through our awareness of this hierarchical system, we are better able to understand how it evolved.
Nothing about mutations or viruses. Nothing about a consciousness guiding these mechanisms.
And they are shared in such a way that it violates a nested hierarchy.
And yet those species share a common ancestor as shown by the evidence.
That appears to be saying the same thing I am.
I can say that invisible pink gravity unicorns are responsible for moving planets around, and my theory predicts (for no apparent reason) that the planets should move through orbits that exactly fit the predictions of general relativity.
Do I have a good theory? Have I shown that invisible pink gravity unicorns are responsible for moving planets around their star? Have I disproven general relativity?
Now wait just one minute: I learned in botany that horizontal gene transfers between species generally result in screwed-up patterns that make the nested aspect fuzzy! If I have a species with genes A,B,C,D,E,F,G and another with H,I,J,K,L,M,N,O, P, and descendant species with A thru G plus Q and R, and H thru P with S and T, if I find a species with A,B,C,D,Q,E,F,T,G,R, the presence of the transferred T makes the nesting untidy.
It seems to me that if HGT were more common, the result would be a lot more ânoiseâ that would make the nested hierarchy less obvious (at best), it wouldnât result in such a pattern.
Iâm seeing a distinction without a difference. Evolutionary biology as of thirty years ago accounted for âboth nested patterns and their exceptionsâ* perfectly well, including a case (in a member of the mint family IIRC) where it wasnât just a gene but an entire chromosome that jumped from one species into another. I donât see any way that your alternative is better, just hand-waving and claiming it to be so.
Oh, nonsense â survival of the fit enough explains it without invoking metaphysics.
How are you defining consciousness when you say this? If you are using our definition of consciousness, then this study on quantum tunneling in microtubules and the other study on quantum tunneling in mutations do provide support for our theory.
Let me explain why the Convergent co-option of viruses in biology is better explained by Owenâs frameworkâŠ
The term âbasic typesâ denotes the complete set of all known living and/or extinct animals, plants, or humans in a group or pair, beginning after the designer formed the original set of kinds that can sexually reproduce. In other words, it refers to an entire related group that (1) shares continuity, meaning that each member is continuous with at least one other member, and (2) is bounded by discontinuity. Therefore, each natural group of related plants, animals, and humankind constitutes a basic type. The basic type may be represented as a branching tree, with the nodes and tips of the branches representing all the known members of the âkind". Essentially, a basic type resembles a clade in evolution, with the distinction that the original kind does not have a common ancestor capable of sexual reproduction. Instead, stem metazoans and microbes are described as common design parts rather than common ancestors. This aligns with Owenâs notion of fundamental forms in the natural worldâreferred to as the Typesâwhich are inherent and governed by the universal common archetype.
While mutations themselves are random, Ayala describes this randomness as âunorientedâ concerning fitness or adaptation; mutations occur independently of an organismâs adaptive needs. However, through natural selection, beneficial mutations are preserved, and maladaptive ones are typically filtered out. This interplayârandom mutation with adaptive, non-random selectionâcreates the order we see in evolution, enabling functional design without intelligent guidance. This process shows that randomness in mutations does not equate to randomness in evolutionary outcomes.
I am not sure what you are getting at here or your point.
So why arenât there any original sets that violates a nested hierarchy? For example, why isnât there an original set that has a mixture of mammal and bird features? Why do the original sets also form a nested hierarchy between them when no such thing is required in your theory?
Thatâs what ârandom with respect to fitnessâ means.
I have proposed that there are invisible pink gravity unicorns that move planets about their star in such a way that the orbits are identical to those predicted by general relativity.
Have I disproven general relativity? Have I found the replacement for general relativity?
How is this different than you claiming some consciousness is responsible for creating groups or kinds in such a way that it exactly mimics what we would expect from common ancestry and evolution for no apparent reason?
Oh ok, I think what I said below will address this comment by default. So just read on for those answersâŠ
Penroseâs Orch-OR model posits consciousness as a non-algorithmic process involving quantum wave-function collapse in microtubules. This aligns with experimental findings, like quantum interaction-free experiments, where observation impacts superpositions without direct interaction, suggesting consciousness itself may drive collapse. Additionally, studies by Aerts, ArguĂ«lles, and Patel demonstrate how quantum theory explains cognitive processes and the structure of genetic code, respectively. Research on electron tunneling in biological systems shows optimized transfer rates beyond classical limits, supporting the role of quantum mechanics in biological stability and evolutionary adaptation.
Observations appear to tell a different story in this study that does show a violation by original sets:
Thatâs true, and it depends on the design objectives. In software, modular design often avoids hierarchical structures for flexibility, but in biology, the analogy might be different. Based on what the study below suggests, we propose that in biology, nested hierarchies could arise due to the efficiency and speed of evolutionary design principles, which often lead to tree-like structures as we observe in phylogenetic data.
I said what I said in combination with the causal role definition of function, which means that it is not the same thing as what you said because you were clearly referring to the selection-effect definition of function.
âŠ
. . . BOOM!