It is falsified by all of the impacts non-consciousness has in quantum mechanics. For example, all of the photons being absorbed by space dust across the universe.
So you are now arguing that your model should not produce a nested hierarchy?
When humans design organisms we regularly violate a nested hierarchy. There is no reason why design would necessarily produce a nested hierarchy.
I am talking about mutations, not selection. The processes that produce mutations do so in a way that is random with respect to fitness. These processes are just as likely to produce a beneficial mutation as they are a neutral or deleterious mutation.
If a consciousness is guiding mutations, then why do we see this? What would it look like if a consciousness is not guiding these mutations?
I believe there may be a misunderstanding here. Our reference to quantum interaction-free experiments serves to define consciousness as the self-collapse of the wave-function, not to suggest that consciousness causes this collapse. The distinction is explored in the section âHuman consciousnessâ of the article, where we clarify that consciousness reflects a self-referential aspect rather than a causal agent for collapse. However, if you promise to eventually endorse our preprint after you wave the white flag in our discussion, then I will copy and paste that section for you.
Our model accommodates both hierarchical and non-hierarchical patterns. As noted, certain nested patterns can arise through mechanisms like convergent co-option and horizontal gene transfer (HGT), processes that introduce complexities beyond strict lineage hierarchies. For example, in synthetic biology, viruses are used to design organisms, which parallels observed patterns in nature but disrupts a strict hierarchy. Similarly, RNA viruses, lacking cellular structure and arising polyphyletically, illustrate exceptions to a Tree of Life model. Thus, our view aligns with Owenâs theory, which accounts for nested structures while also addressing these deviations.
Weâve included studies showing that viruses both mimic and disrupt nested structures, serving as examples of engineered and natural parallels. Additionally, viruses are utilized in synthetic biology to design organisms, underscoring the parallels between human-engineered patterns and those found in natural systems.
Our model does not assert that design will necessarily produce a nested hierarchy. Instead, it hypothesizes that a nested pattern may emerge if the design goal aligns with optimizing organisms for survival, reproduction, and environmental integration. This is an initial hypothesis and one that we propose future studies could test to refine our understanding of nested hierarchy patterns in designed systems.
I see the distinction you are drawing, and I refer to a slightly different interpretation of ârandomâ as it applies to mutation. Ayala notes two meanings of randomness in evolutionary context. Youâre describing Ayalaâs second definition, âthere is no way of knowing which gene will mutate in a particular cell or in a particular individual,â highlighting the uniform likelihood of various outcomes. This meaning of randomness aligns with your statement, but it is not what I was referring to.
According to the universal common design theory, the designer is seen as omnibenevolent, designing all nephesh basic type animals along with humans to survive, reproduce, and/or adapt throughout history. Therefore, the designer would not design them with pathogens or features that reduce the population or another nephesh basic type or humanâs ability to survive, reproduce, and fit in an environmental niche. However, there are many current examples in nature that conflict with the theory.
In the future, research will seek to verify that alleged âharmfulâ design features contribute to a measurable increase in the efficiency and speed of a population or another nephesh basic type animal or humanâs survival, reproduction, and adaptation. This prediction implies that features traditionally considered harmful or detrimental actually contribute to the efficiency and speed of survival, reproduction, and adaptation in populations. This is also a methodology for testing our design model for nested patterns.This approach diverges from Darwinian views that emphasize individual fitness over group survival and resilience, particularly in cases involving harmful or neutral mutations.
I doubt that, since (i) itâs not freely available, and (ii) its a book chapter, not an article. I suspect you read at most the introduction, a couple of snippets from other sections, and the conclusion.
You could refute me by quoting some part of the chapter that is not available here.
I doubt that too. The chapter is about using changes to gene regulatory networks in sea urchins to understand the evolution of complex systems. It is not about software engineering principles or nested hierarchies. None of the abstract, introduction, conclusion or additional snippets available at the above link even mention software engineering, code reuse, scalability or nested hierarchies. âSoftwareâ, âcodeâ, âreuseâ, âscalabilityâ and âprinciplesâ arenât there at all; âengineeringâ occurs once in a list of academic disciples; âmaintenanceâ is applied once to biological units and ânestedâ is applied only to interactions and modules.
Unless you can cite additional text from the article that actually mentions software engineering principles and nested hierarchies, there is no reason to believe you when you say that this article supports âsoftware engineering principles ⊠are closely tied to the concept of nested hierarchyâ, and multiple reasons[1] to reject it.
So Iâm rejecting that claim until you can provide an extract from that article that mentions software engineering principles, nested hierarchies, or preferably both.
[1] Even without knowing of your extensive known record of lying about both the nature and contents of your cited sources, which record has apparently just been extended.
âYour honor, if you find the defendant guilty I would be happy to present evidence for my case.ââNo Prosecuting Attorney Ever
We observe vertical inheritance and common ancestry producing nested hierarchies. The evidence is consistent with these processes.
Viral insertion of DNA is a natural process. We observe it to be so. There is nothing engineered about it. That humans happen to take advantage of a natural process to change genomes doesnât change this fact.
I am not saying that. I am saying that mutations are random with respect to fitness. This means organisms are not capable of producing specific mutations in response to specific stimuli. For example, bacteria donât specifically produce mutations that confer antibiotics when they are exposed to antibiotics. This observation was made by the Lederbergâs in their famous paper:
This paper was written in 1952, well before we had a solid understand of what mutations looked like at the molecular level. When mutations were first described as being random it was in reference to the appearance of a phenotype in relation to the environment.
You are aware of genetic diseases, right? Are you aware of those that cause death in childhood, like Tay Sachs? Until recently, cystic fibrosis led to death in childhood. Are you really going to try and see how these are actually beneficial?
Iâve now read it (thanks to the Harvard Library, from which I could get a copy online).
You are correct. The chapter says nothing about human designs and very little about why modularity (which is a bigger focus than hierarchy) is useful â or at least the reader can infer that itâs useful. On the other hand, one notable point in the chapter is that modules are often reused in different developmental contexts in the same organism, i.e. identical complex molecular systems are used repeatedly in ways that violate the hierarchical structure of development. This is notable because we do not see a similar violation of the phylogenetic tree; that is, we donât see identical, complex systems deployed in two distant branches of the tree without also being deployed in intervening branches. Which is what has been said here repeatedly.
No, this is not a valid analogy or example because I provided the evidence already. What you want is specific details to help you understand the evidence better. Again, I expect mutual effort. If you are promising a potential endorsement, then I will copy and paste that very large excerpt from the article so you can fully understand our overall case. BTW, what exactly is your expertise and qualifications?
Reproducibility: In nature, convergent co-option and gene duplication or horizontal gene transfer (HGT) can be likened to âcode reuse,â where genetic components are conserved and repurposed across different organisms [33,50,82]. This phenomenon often results in nested patterns, observable even in viruses. This means that we do observe common design producing nested patterns as well:
G.P. Fournier, C.P. Andam, J.P. Gogarten, Ancient horizontal gene transfer and the last common ancestors. BMC Evol. Biol. 15, 70 (2015).
A. Phillips et al., Hierarchical sequence-affinity landscapes shape the evolution of breadth in an anti-influenza receptor binding site antibody eLife 12, e83628 (2023).
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), PMID: 36240227, PMCID: PMC9604959.
As we pointed out in the article, reconciling the likely natural origin and evolution of viruses with Darwinâs theory of evolution poses challenges, as viruses cannot survive or evolve independently from their hosts through natural selection, nor can they be classified within the Tree of Life. However, Owenâs extended theory offers a plausible explanation for these phenomena, supported by evidence of humans essentially replicating these effects in real-time experiments. This approach is grounded in the principle of causation from past events, popularized by Charles Lyell. Lyell argued that explanations for past events should rely on causes known from our uniform experience to produce the observed effects. Darwin also embraced this methodological principle, aiming to demonstrate that natural selection was causally sufficient to explain the effects observed in past events.
Remember Ayalaâs definition. He specifically said mutations are âunorientedâ regarding adaptation AND occur without regard to benefit or harm to organisms. The second part does not align at all with what you said. It specifically referring to mutations not natural selection or the environment.
I forgot to point out that examples of pain, suffering, and death that results from natural disasters or disease stemming from poor decisions and human moral failings [2,32,75] do not count as malevolent designs or conflict with the theory. Examples of design decay or design trade-offs in nature [51] also do not count as design flaws or conflict with the theory. For instance, the designer cannot create a universe without decaying effects because the second law of thermodynamics is a fundamental principle that applies to all physical systems [1], including those described by quantum mechanics [1], which means the law probably exists in all possible worlds. Cancer would fall into this category because it reflects design decay [51] and a trade-off between DNA repair and cell survival [51]. Therefore, under these circumstances, the designer would not be held responsible for a genuine design flaw or a cruel design feature.
Read the fifth paragraph of this article to find this paragraph:
Interesting comparison. How may some quantum processes be affected by consciousness? Miracle healing and coincidences become more likely for the naturalist or an open topic for methodological naturalism.
I read it. I also read Section 3.2, starting with âthere are many examples of circuits being deployed in different spatio-temporal contexts to perform novel tasksâ and then proceeding to a detailed discussion of the different ways that genes or entire gene regulatory circuits are reused in different contexts â which is the point I was explicitly making.
Correct, no intelligent designer necessary. Natural processes are completely capable of producing what we observe.
We can observe viruses inserting into host genomes. It is an entirely natural process, no designer required.
We also observe that viruses insert randomly within the genome.
Again, parsimony matters. We already have a natural process that explains the data. Inventing a supernatural process that exactly mimics the natural one is a dead end.
Yes. The natural process of viruses inserting into genomes.
Yes, it does.
It would appear that no evidence can ever conflict with your theory. Unfalsifiable models arenât scientific.
When we talk about a nested hierarchy we are talking about the organization of species based on their morphology and DNA sequence comparisons, not the organization of gene regulatory pathways within the genome.
Yes, one can make that analogy, but since itâs something thatâs easily explainable in evolutionary terms without any reference to design. What would not be explainable in those terms would be the reappearance of the same complex molecular mechanisms in distant parts of a phylogenetic tree. That is something that we do see all the time with intelligently designed systems and never see in biology. Itâs the thing (or rather, one of the things) that you keep ignoring.
No. It does contain the word âcomputerâ once, when introducing the concept of modularity: âThe concept of modularity is widespread across multiple academic disciplines, including engineering, computer science, mathematics, biology, and architecture (Simon, 1962). In all of these fields, modularity provides insight into the structure, and in some cases the evolution, of complex systems.â
From my reading of this thread all you did was say âThe evidence is over thereâ. In the context of this sort of discussion, âto provideâ is equivalent to âto quoteâ, which means actually posting the material that is considered to be evidence.
Looks to me like it contradicts it: just because humans can do it one way does not mean thatâs how it actually happened.
So? I used to use modules when assembling large LEGO structures. That doesnât mean that LEGO bricks are related to biology or to software.
Make sure you read the whole thing so you can understand the evidence better, if possible:
Roger Penrose posits that consciousness stems from orchestrated objective reduction (Orch-OR), involving the collapse of quantum wave functions within microtubules [28,29,43]. This process, distinct from algorithmic processes, enables consciousness to perform tasks beyond computational abilities, such as contemplation and freely making moral and intellectual judgments [28,29,43].
The only known phenomenon in nature capable of achieving this is a wave function collapse [28]. At small scales, quantum particles exist in multiple states or locations simultaneously, described by a mathematical equation known as a quantum wave function. However, these superpositions are not observable in our everyday world. Early 20th-century double-slit experiments indicated that observation causes superposition wave functions to collapse to definite states, selecting a particular reality. This unobservable nature of quantum superpositions is referred to as the measurement problem, thought to be somewhat associated with consciousness [28].
For instance, before observation, an observer lacks knowledge about both the location and timing of a particleâs appearance. Mathematical wave functions are employed to describe the particleâs properties, detailing its location and momentum. The measuring apparatus is then used to unveil the particleâs whereabouts and movement. The observer plays a crucial role in this process, as they must specify a particular wave function they intend to measure and set up a measuring device designed to probe that aspect. When a conscious observer decides to measure a quantum system, the particles suddenly manifest and exhibit classical behavior, leading to what is known as wave-function collapse. This concept aligns with the findings of a âquantum interaction-freeâ experiment, where the position, presence, or state of an object was detected without direct interaction between the quantum system and the measuring device [45]. Overall, this is why Penrose defines consciousness as the self-collapse of the wave function [28,29,43].
Furthermore, Aerts and ArguĂ«lles (2022) have shown how quantum theory can be applied to model various cognitive processes, including decision-making, conceptual reasoning, human judgment, and perception [102]. Recent studies have also suggested that specific conditions within neural networks can lead to the emergence of quantum-like behavior [38]. This behavior exhibits connections to the mathematical framework of quantum systems, leading some researchers to propose that physical reality itself may be describable at a fundamental level as a neural network [38]. While this proposal doesnât necessarily imply a direct correspondence to biological neural networks, Kurtev [38] argues, based on existing experiments, that there is evidence supporting a real correspondence. This is achieved through a deep analogy between neural network parameters and physical systems, along with the presumed existence of a causal mechanism allowing certain bird species to sense Earthâs magnetic field orientation via quantum effects occurring on a microscale [38]. Penrose introduced a causal mechanism for this process, positing a direct correspondence between quantum phenomena and consciousness [28,29,43]. According to his theory, quantum information is processed by microtubules and then âorchestratedâ by the brain to produce a coherent conscious experience [28,29,43].
While Penroseâs Orch-OR model proposes consciousness as the result of the spontaneous and non-computable collapse of the universal wave function, our perspective shares this premise while differing in explanations for the mechanism of collapse and the role of gravity in shaping quantum phenomena. Penroseâs model posits gravitational effects, particularly at the Planck scale, as leading to objective reduction, wherein the wave function collapses due to gravitational self-energy [28], although the precise mechanism remains speculative [22]. In contrast, we suggest gravity as an inherent aspect of the quantum wave-function, proposing that non-local consciousness interacts with gravitational effects at the quantum level to induce collapse events, with quantum fluctuations in the form of dark energy playing a key role in this process. Another notable distinction lies in the modelsâ explanations for the origin of the universe: Penrose adheres to Conformal Cyclic Cosmology [43], while Owenâs extended theory aligns with eternal inflation.
While other structuralists may not align with quantum consciousness theories, they have also proposed that microtubules represent another instance of a molecular form that evidently emerges from the inherent self-organizing properties of its fundamental constituents [21]. This perspective mirrors Richard Owenâs implementation of divine agency into his common archetype theory, wherein intentional acts of a divine Creator are invoked to explain the existence and organization of biological structures and forms [21]. This framework provided a basis for understanding the natural world as the product of intelligent design, with each species reflecting the Creatorâs purpose and intention, contrasting with purely mindless naturalistic processes such as evolution by natural selection [21].
For instance, every living creature on Earth uses the same code: DNA stores information using four nucleotide bases. The sequences of nucleotides encode information for constructing proteins from an alphabet of 20 amino acids. But why were these specific numbers chosen rather than some other numbers?
Patelâs work sheds light on this question by drawing parallels between the genetic code and quantum algorithms. Patel argues that the genetic codeâs structure, consisting of 64 codons encoding 20 amino acids with redundancy, mirrors the mathematical framework of quantum algorithms [59]. This redundancy allows for error tolerance in DNA replication while maintaining accuracy in protein synthesis, a feature similarly found in quantum algorithmsâ efficient computation with error tolerance [59]. Patel proposes that the genetic code evolved to harness quantum coherence effects during DNA replication and transcription, enhancing the accuracy and efficiency of protein synthesis through natural selection acting on quantum-mechanical properties of DNA and RNA molecules [59]. Recent experiments have even demonstrated the fundamental nature of this quantum search algorithm [66].
Furthermore, in the article âNatural engineering principles of electron tunneling in biological oxidation-reduction,â authors discussed electron transfer mechanisms in biological systems, pivotal for energy production and metabolism [57]. They proposed that biological electron transfer systems exhibit engineering principles akin to those in artificial electronic devices, such as transistors and diodes [57]. Specifically, they suggested that electron transfer in biological systems relies on quantum tunneling, enabling electrons to traverse barriers that would be classically insurmountable [57]. The authors further described how observed electron tunneling principles in biological systems are highly optimized, with transfer rates surpassing expectations based on classical tunneling theory [57]. While ongoing discussions regarding tunneling in DNA bases persist, current literature consistently validates the existence of this crucial process [83].
You are confusing the intelligent design theory posited by the Discovery institute with Owenâs theory. They are not the same because Owenâs theory still involves natural processes. It is just natural law rather than natural selection.
Well, Owenâs theory predicts it was a non-random insert by a designer or consciousness. This is the prediction:
Dynamic microtubule vibrations correlating with viral activity
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.
I donât see how then.
To start, I donât see how this makes the prediction automatically unfalsifiable; rather, it simply sets clear parameters for a meaningful falsification. Moreover, if this approach is considered unfalsifiable, then by similar reasoning, Darwinâs theory could also be deemed unfalsifiable. This is due to the argument that the fossil record may never provide a complete enough history to fully validate common descent, given the inherent limitations of fossilization.
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.
However, our model accommodates both hierarchical and non-hierarchical patterns. As noted, certain nested patterns can arise through mechanisms like convergent co-option and horizontal gene transfer (HGT), processes that introduce complexities beyond strict lineage hierarchies. For example, in synthetic biology, viruses are used to design organisms, which parallels observed patterns in nature but disrupts a strict hierarchy. Similarly, RNA viruses, lacking cellular structure and arising polyphyletically, illustrate exceptions to a Tree of Life model. Thus, our view aligns with Owenâs theory, which accounts for nested structures while also addressing these deviations.
You must be careful to distinguish web from tree structures, although they can mix. Tree structures, or nested hierarchies, are defined both by traits which are present, and traits which are absent. The presence of a foreign trait imported from the tip of distant branch violates the nested hierarchy. Nature can do that via HGT, but then the connection between the organisms is a web rather than a branch, although from that point forward, that trait can be carried forward on the branch and subsequent forks.
As programmers here have stated, computer programs generally violate nested hierarchies, so that is not a competent analogy. If you want to somehow draw a connection to computers, files are addressed by tree structures, and are nested. All the files in a sub directory are also in the directory containing the sub directory, and also belong to the root containing the directory, and so forth. I do not think that yields much insight into biology, however.
Seems to me this is a good spot to quote something I posted some time back:
A Psalm of the Designer
Evolution declares the glory of God, and the chromosomes in cells proclaim His handiwork! Day to day pours out research, and night to night reveals studies. They have no speech, they use no words; no sound is heard from them, yet their message has gone out to the whole earth, and their words to the ends of the world. He has set a tent for DNA, which sends its messengers out from its chamber like strong men they run their course with joy. Its reach is from the birth of the Earth, its circuit all around it, and there is no life apart from that reach. selah
O Lord, our Lord, how majestic is your name in all the earth! You have set your glory within the cell. When I look at all life, the work of your fingers, the nucleus and the mitochondria§, which you have set in place â What is man that you are mindful of him, and the son of man that you care for him? You have made them a little lower than the angels and crowned them with glory and honor. You made them rulers over the works of your hands; you put everything under their feet: all flocks and herds, and the animals of the wild, the birds in the sky, and the fish in the sea, all that swim the paths of the seas. Oh Lord, our Lord, how majestic is your name in all the earth!
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.
However, our model accommodates both hierarchical and non-hierarchical patterns. As noted, certain nested patterns can arise through mechanisms like convergent co-option and horizontal gene transfer (HGT), processes that introduce complexities beyond strict lineage hierarchies. For example, in synthetic biology, viruses are used to design organisms, which parallels observed patterns in nature but disrupts a strict hierarchy. Similarly, RNA viruses, lacking cellular structure and arising polyphyletically, illustrate exceptions to a Tree of Life model. Thus, our view aligns with Owenâs theory, which accounts for nested structures while also addressing these deviations
