Need reviewers for Common Design theory to be submitted to Science journal

Faith & Science Conversation
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I find it hard to believe that anyone who has written code for a living thinks that software develops in a nested hierarchy. Indeed, one of the main reasons that software engineering relies on modularity is that it allows developers to violate a treelike development pattern at will.

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Our theory posits consciousness as the self-collapse of the universal wave function, which aligns with established findings and predictions from Orch-OR theory:

  • Quantum Coherence in Microtubules: Orch-OR predicts quantum coherence (the preservation of quantum properties) in brain microtubules, which has been directly supported by experiments showing quantum vibrations in microtubule molecules, suggesting coherence under biological conditions.
  • Microtubules and Quantum States: Research demonstrates that microtubules contribute to critical cognitive functions, supporting Orch-OR’s claim that microtubules process quantum states relevant to consciousness.
  • Quantum Vibrations in Microtubules: Orch-OR proposes that microtubules exhibit vibrational modes to support quantum processing. Observed resonant vibrations at brain-relevant frequencies (EEG frequencies) align with Orch-OR predictions of quantum processing in microtubules.
  • Orchestrated State Reduction Timing: Orch-OR posits consciousness arises from the periodic “collapse” of quantum states within microtubules at frequencies matching EEG (10-40 Hz). Empirical evidence supports a connection between these frequencies and consciousness.
  • Anesthetics and Quantum Processes: Orch-OR predicts that anesthetics disrupt quantum coherence in microtubules, leading to loss of consciousness. Studies show that anesthetics affect microtubule dynamics, likely impacting coherence.
  • Tubulin Dipole Oscillations: Orch-OR suggests tubulin proteins in microtubules act as quantum bits (qubits) through dipole oscillations. Studies indicate that tubulin dimers exhibit dynamic dipole behavior needed for quantum processing, potentially serving as biological qubits.

Increasing evidence supports quantum processes occurring in the brain, as seen in [sources 29, 36, 38, 43, 92]. This body of research strengthens quantum consciousness theories overall.

Further, evidence from the study “Natural engineering principles of electron tunneling in biological oxidation-reduction” describes quantum tunneling mechanisms essential for biological electron transfer, which is necessary for cognition and metabolism [57]. This aligns with our model that consciousness actively guides these processes. For instance, recent experiments show tubulin proteins self-assembling, crucial for forming microtubules, under specific electromagnetic signals, confirming the relevance of quantum effects in cellular assembly and function.

Overall, this is why the confirmed predictions on the fine-structure constant is relevant to our theory since it is integral to electromagnetic interactions between charged particles. Any deviation in this constant would alter atomic interactions, potentially rendering complex life impossible. This model supports our theory: constants that allow for existence also support evolutionary processes, integrating “causal necessity” into evolutionary frameworks.

The evidence supports our view in the following ways


Many structuralists argue that the fine-tuning constants offer evidence of a deeper underlying structure or intelligence in the universe [21,28], echoing the beliefs of Richard Owen and other scientists of his era in the existence of a polarizing force or organizing energy that directed the development and growth of organisms. This vital force was perceived as a guiding principle responsible for the organization and functioning of living matter [21]. Modern structuralists propose that the values of these dimensionless constants, which determine the physical laws and properties of the universe, are not arbitrary but finely tuned to allow for the emergence of life and consciousness [21,28]. Some go further, suggesting that these values have ‘self-organized’ and ‘evolved’ over cosmic time spans [28].

Observations on the fine-tuning constants seem to support both perspectives [30,52]. For example, there is no evidence of variation in the fine-tuning constants [30], which would suggest a random or arbitrary process [28]. Moreover, using the Planck scale Wilkinson Microwave Anisotropy Probe, researchers have shown that the fine-structure constant in physics has remained constant throughout the universe’s history [52].

The cosmological constant is another indicator of precise design and causal necessity, measured at an extraordinary 10^120 and refined to 10^(10^123) within a second of the universe’s origin [5]. Moreover, studies show that dark energy’s influence aligns with relativity, impacting universal expansion and even the formation of sub-universes [79]. Further, if the expansion rate deviated due to changes in dark energy, it could prevent habitable planet and star formation necessary for life [104,105].

In our model, such fine-tuning supports a continually active consciousness. Consciousness may not only set these constants but interact with them, sustaining conditions for life. Experimental evidence suggests wave-function collapse, induced by conscious observation, aligns with observed quantum interactions where specific conditions—like the cosmological constant—are maintained. This parallels findings in ‘interaction-free’ quantum experiments where objects are detected without direct measurement and the functional similarities observed between quantum systems and human cognitive processes, hinting at consciousness’s role in maintaining constants rather than decoherence theory or string theories’ multiverse

Our model proposes that consciousness isn’t only “front-loaded” but sustains these constants, keeping them within ranges compatible with life and the universe’s stability.

Observations seem to suggest otherwise


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?

Patel’s research proposes that this genetic code mirrors quantum algorithm frameworks, especially in its redundancy, which tolerates replication errors while preserving protein synthesis accuracy.

In this way, the genetic code would be viewed as an “emergent” system that exploits quantum principles, which, in turn, are shaped by fundamental physical laws. This would be a fascinating example of how biological systems can reflect and utilize fundamental physical principles. This further integrates “causal necessity” into evolutionary frameworks.

While deductive reasoning indeed makes this argument fallacious, ENCODE’s reasoning was based on inductive reasoning. In scientific induction, conclusions are probabilistic, allowing scientists to ascribe function to sequences binding transcription factors based on observed probability, not absolute certainty. This methodology, while not flawless, remains a staple of scientific practice, including in the ENCODE study.

Given the extensive data showing transcription factors bind specific DNA sequences regulating gene expression, ENCODE’s conclusion remains a probable explanation. Though alternative theories exist, further experiments can narrow uncertainty around function in genome binding, reinforcing ENCODE’s perspective.

Criteria for Disconfirming Claims
To refute these hypotheses, one would need to disprove the following correlations:

  • Synaptic plasticity with cytoskeletal structure
  • Viral activity with dynamic microtubule patterns
  • Memory stability with microtubule patterns
  • EPR-like non-local correlations in separated microtubules

That was not the question you asked. You said, Why would a nested hierarchy emerge if design goals align with optimizing organisms for survival, reproduction, and environmental integration?

The answer: Because software engineering principles like easier maintenance, code reuse, and scalability are closely tied to the concept of nested hierarchy.

We would anticipate a universal common design among species, as the natural origin and design of viruses (see ref. 255 and 87 [50]) appear to mirror the artificial synthesis and design of viruses [97].

For example, researchers can redesign or refactor the genome of bacteriophage T7 to create an engineered surrogate optimized for human purposes, such as resistance to virus infection—a process observed in nature [97]. This showcases how genomes encoding natural biological systems can be systematically redesigned and rebuilt to serve scientific understanding or human intentions [97]. In one instance, scientists synthesized RNA molecules of a virus and reconstructed a poliovirus particle from scratch, without a natural template [97]. This was achieved by utilizing components from another virus, such as specialized proteins (enzymes), to construct an RNA virus capable of addressing the problem of unstable RNA [97]. Upon introducing this synthetic RNA virus into cells, it successfully generated infectious poliovirus particles [97]. The instability of RNA is a well-known challenge in the RNA world hypothesis, and similar solutions have been proposed, such as the Protein-first hypothesis [7].

Furthermore, observations suggest that RNA viruses not only likely preceded the first cells [25, 50] but also played a crucial role in shaping and building the genomes of all species [25,50]. HGT can confer significant advantages to organisms, enabling them to overcome challenges that would otherwise require gradual evolution through mutation and selection [25,50]. This suggests that evolution can be accelerated as a parallel process, wherein innovations originating in different lineages converge in a single cell through HGT [25,50].

In contrast, the concept of a universal common descent among species is not supported due to limitations in natural selection’s ability to explain the transition from non-life to life or to differentiate between non-living and living entities [93]. Particularly, RNA viruses cannot be integrated into the Tree of Life framework because they lack cellular characteristics [50], and no single gene is universally shared among all viruses or viral lineages [50]. Viruses are polyphyletic, having multiple evolutionary origins [50]. Moreover, the presence of horizontally transferred genes in organism genomes can complicate phylogenetic relationships, deviating from the clear vertical inheritance depicted by the Tree of Life [15,25]. This phenomenon blurs the lines of evolutionary descent, as genes from diverse sources may coexist within the genome of a single organism [15,25]. As a result, establishing a singular common ancestry for an organism based solely on its genes becomes challenging [15,25].

Therefore, reconciling the likely natural origin and evolution of viruses with Darwin’s 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 [50,93]. However, Owen’s extended theory offers a plausible explanation for these phenomena [21], supported by evidence of humans essentially replicating these effects in real-time experiments [97]. This approach is grounded in the principle of causation from past events, popularized by Charles Lyell [94]. Lyell argued that explanations for past events should rely on causes known from our uniform experience to produce the observed effects [94]. Darwin also embraced this methodological principle [94], aiming to demonstrate that natural selection was causally sufficient to explain the effects observed in past events [94].

For instance, mitochondrial and chloroplast DNA are abundantly involved in apoptosis, which is the single most important feature of multicellularity because it ensures timely death of individual cells. Cancer may be the ecological equivalent of apoptosis, ensuring the timely death of individuals so that resources are available for the young. Also, sickle cell disease has been shown to confer a survival advantage against malaria, the disease caused by Plasmodium infection (Ferreira et al., 2012).

While Tay-Sachs and cystic fibrosis don’t offer direct adaptive advantages in the same way, the persistence of certain deleterious mutations in populations may be due to genetic drift or historical selective pressures that once favored heterozygous carriers. This could lead to a more nuanced understanding of how not all mutations confer a current population-level benefit but may still reflect complex evolutionary dynamics.

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I find it hard to believe that anyone who has taken more than two university-level computer science courses would think so. We swapped sections of code back and forth and reused whatever worked.

Yep – the software equivalent of “plug and play”. Doesn’t matter if Tim or Ivan or Shem or Jens wrote a module, if it fits and works with whatever Tina or Irene or Sharon or Jane is writing you slap it in and go with it.

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I am not convinced that nested hierarchies in software architectures have any applicability to the nested hierarchy of say the evolutionary tree of life in Biology. Perhaps I am misunderstanding.

Can you point to any sources that develop in a precise way this notion of a relationship, by nested hierarchies, between software systems and biological systems?

The architecture of a particular complex software system will have hierarchies (not necessarily nested) of components, in the sense of layers of complexity. For example, the application programming interface (API) will sit “above” the modules that implement the functionality of the system, which will sit “above” low-level modules tailored to particular chip architectures, and so on.

Another example is the Open Systems Interconnection (OSI) model of communication networks (OSI model - Wikipedia). This is a 7 layer architecture, with an “application” layer at the top, down to the “physical” layer at the bottom.

But nested hierarchies DO NOT occur among diverse software systems, or even in the “evolution” of a particular software system. Take the Microsoft Windows Operating System as an example. I would not expect (not from direct experience) that there is any nested hierarchy of the code between say Windows 3.1, Windows NT, and Windows 10 or 11. I would expect that virtually all of the code has been “thrown away” at various times as the operating system has evolved over the years.

I have worked as a software engineer on a large complex system, and at various times large parts of the system were completely re-written as it evolved.

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Yes, I think that might be the reason because our model does not assert that design will necessarily produce a nested hierarchy. Instead, based on observations and experiments on viruses, we hypothesize 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.

G.S. Hornby, Modularity, reuse, and hierarchy: Measuring complexity by measuring structure and organization. Complexity 13, 50–61 (2007).

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As I’ve already pointed out, that chapter does nothing at all to develop (precisely or not) the notion of a relationship between software systems and biological systems.

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Sorry, I forgot you said this. Can you tell me whether the other source is the same way, or can you not get access to it as well because there is a paywall? I will replace it as well if it does.

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All you need is the reproduction, and the nested pattern will ensue.

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Admission of citing sources that haven’t been read noted.

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This paper is here:
https://onlinelibrary.wiley.com/doi/abs/10.1002/cplx.20202

which is behind a paywall. From the abstract, it’s not at all obvious that the author is making a connection between software systems and biological evolution.

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@RTBsupporter has been caught misrepresenting his sources[1] so often, so frequently and so blatantly that the default assumption about anything he cites should be that he hasn’t read it, he doesn’t know what it’s about, and doesn’t support anything he said, and any ‘quote’ won’t match the actual text.

If anyone has doubts, just note that he asked @glipsnort to tell him what his own source says.

  1. Examples available on request. ↩

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He is not.
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filler text to make forum software happy
]

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Strange things happen when you start at the conclusion.

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Shouldn’t you already know this? How can you handle citations without knowing what’s in them?

In any case
 the Hornby paper alludes to similarities between natural and artificial objects but does not address them in any way.

One of the many problems with the Common Design paper is that it conflates the nested hierarchies within an organism (e.g. organelle, cell, tissue, organ, organism) with the nested hierarchy among organisms (species, genus, family, etc). The former has some similarities to the nested hierarchies in designed objects, the hierarchies that Hornby’s paper addresses. The latter doesn’t, and the latter is what provides evidence for common descent.

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You have yet to produce evidence for this. All you do is point to quantum effects, but no evidence that this is producing a consciousness. Nor have you produced evidence that this consciousness is guiding mutations, or even how you would detect this.

Arguments aren’t evidence.

None of which existed for the first 9 billion years of the universe. Reality’s structure does not require DNA.

What probability?

You are committing the same logical fallacy.

None of which you can tie to DNA in any meaningful manner.

That answer has been refuted multiple times now.

That’s gobbleygook.

Just because humans use viruses does not mean viruses were designed.

A designer opted for an adaptation that would result in horrific disease in homozygotes? Yikes.

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You are largely correct in pointing out a need for evidence still, but there seems to be a misunderstanding about the framework of our model. Our definition of consciousness integrates quantum effects and positions it as a fundamental force interacting with biological processes. Without grasping this foundational definition, it’s difficult to appreciate how our theory aligns with real-world data. For examples


First Study: Sahu S, Ghosh S, Fujita D, Bandyopadhyay A. Live visualizations of single isolated tubulin protein self-assembly via tunneling current: effect of electromagnetic pumping during spontaneous growth of microtubule. Sci Rep. 2014 Dec 3;4:7303. doi: 10.1038/srep07303. PMID: 25466883; PMCID: PMC4252892.

Relevance to Consciousness and Mutation Guidance:

  1. Microtubules as Quantum Structures: As I mention before, the self-assembly of tubulin into microtubules is a foundational event in cellular structure and function. The fact that this process can be influenced by electromagnetic signals and quantum tunneling suggests that microtubules would be sensitive to quantum-level manipulations, which are proposed in theories of quantum consciousness (e.g., Orch-OR model).
  2. Consciousness and Electromagnetic Fields: If consciousness operates at a quantum level and interacts with microtubules through quantum phenomena, then electromagnetic signals would theoretically serve as a medium through which consciousness would influence or regulate cellular processes, including mutations.

Second Study: Slocombe L, Winokan M, Al-Khalili J, Sacchi M. Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism. J Phys Chem Lett. 2023 Jan 12;14(1):9-15. doi: 10.1021/acs.jpclett.2c03171. Epub 2022 Dec 23. PMID: 36562711; PMCID: PMC9841559.

Relevance to Consciousness and Mutation Guidance:

  1. Quantum Tunneling in Mutation Formation: The study shows that proton transfer via quantum tunneling in DNA bases can significantly increase mutation rates. This aligns with the idea that quantum phenomena play a critical role in genetic processes.
  2. Consciousness as a Guide for Mutations: If consciousness can influence quantum events, it would guide neutral mutations occurring through quantum tunneling. This would happen when consciousness interacts with the quantum states involved in DNA replication or repair.

Conclusion:

Using the causal role definition, these studies can be interpreted to directly support the idea that consciousness guides mutations. The foundational role of constants like the fine-structure constant ensures the stability necessary for both life and consciousness to operate. This integration positions consciousness as a necessary causal agent in the evolutionary process, directly influencing mutations through its interaction with quantum biological mechanisms. This framework not only strengthens the theoretical basis but also provides a pathway for empirical validation.

For instance, researchers could employ advanced imaging techniques like super-resolution microscopy to visualize synaptic and cytoskeletal ultrastructure. They could stimulate synaptic activity and monitor changes in synaptic strength while observing cytoskeletal alterations. Statistical analyses could reveal correlations between synaptic plasticity and cytoskeletal features. Additionally, genetic or pharmacological manipulations could assess the effects of cytoskeletal components on synaptic plasticity, providing insights into how microtubule dynamics influence cognitive functions and consciousness.

Furthermore, researchers could conduct experiments using animal models to assess memory performance following manipulations of microtubule stability. Visualizing microtubule patterns in neurons before and after memory-related tasks and statistical analyses could determine correlations with memory function. Pharmacological interventions targeting microtubule dynamics could further validate these findings.

In contrast, cognitive science and neuroscience offer alternative explanations for observed parallels between quantum systems and human cognition, focusing on neural network dynamics and information processing.

Again, context is crucial. These studies provide empirical data that align with the theoretical framework of consciousness influencing biological processes. They show that quantum phenomena crucially impact cellular and genetic stability, directly supporting our model. Now, I will show you that real world data comes from this study


  • The fine-structure constant is measured with extreme precision (81 parts per trillion), showing remarkable consistency. This constant governs the electromagnetic interaction between light and charged particles, which is fundamental for the stability of atoms, molecules, and consequently, life.
    Morel, L., Yao, Z., CladĂ©, P. et al. Determination of the fine-structure constant with an accuracy of 81 parts per trillion. Nature 588 , 61–65 (2020). Determination of the fine-structure constant with an accuracy of 81 parts per trillion | Nature

  • Connection to Consciousness: The precision of this constant and its role in fundamental interactions are crucial. Since consciousness is linked to wave-function collapse or other quantum phenomena according to experiments, its interaction would be responsible for maintaining such precise constants by keeping them within life-permitting ranges compatible with life and the universe’s stability.

  • Real-World Data: The measured stability and precision of this constant, especially when discrepancies suggest new physics, provide evidence that something beyond known forces—most likely consciousness—is at play in maintaining the universe’s fundamental constants.

I was actually more so responding to the claim that there is no connection to DNA sequence rather than the other claim. The study does indeed show a connection between quantum mechanics and the genetic code. I don’t know what you mean or getting at with the claim that “Reality’s structure requires no DNA at all”.

The inference to the best explanation suggests that a design model offers a more probable explanation for the observed fine-tuning of constants and their role in sustaining life, compared to chance. FYI, this is inductive reasoning, which would not be a fallacy in this case.

That is not exactly how the argument is constructed. Let me construct it this way


Premise 1: Viruses can be created and designed by the universal common designer described by our theory.because humans essentially replicate these effects in real-time experiments [97]. This approach is grounded in the principle of causation from past events, popularized by Charles Lyell [94]. Lyell argued that explanations for past events should rely on causes known from our uniform experience to produce the observed effects [94]. Darwin also embraced this methodological principle [94], aiming to demonstrate that natural selection was causally sufficient to explain the effects observed in past events

Premise 2: Unguided processes, according to observations and experiments, cannot account for the likely origin or complexity of viruses.

Conclusion (Inductive): Therefore, it is likely that viruses were designed by this universal common designer.

Furthermore, software engineering principles—such as easier maintenance, code reuse, and scalability—are closely tied to the concept of nested hierarchies. Engineers use nested hierarchies to design complex systems more efficiently. Similarly, human-designed viruses often exhibit nested hierarchies, reflecting structured organization.

If the design goals in biological systems are to optimize organisms for survival, reproduction, and integration into their environments, it follows that nested hierarchies would naturally emerge as a result of intentional design. This structured complexity would mirror the efficiency and adaptability observed in human-engineered systems.

That is not how I would describe it. 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.

This suggests that suspension of the second law (i.e., a miracle) would be required to prevent them from occurring at all. According to our theory, the laws of the physico-chemical world are a reflection of this designer’s personal nature and, thus, we would not expect a miracle to happen. Instead, we would expect the designer to remain consistent and use the laws of nature to eliminate these instances. This involves editing and limiting the harmful genetic changes and regulating harmful mutations that do arise in a way that preserves a balance between predator and prey populations because too many predators or prey can cause a collapse of the ecosystem.

The reason for all this is because we used ChatGPT and we had peer-reviewers evaluate whether the sources are consistent with the claims to compensate for not having access to all the articles to read and (potentially) lack of understanding of this field. Here is a snippet of one of those reports:

Strength of the Argument [Rating: Good]

The current version of the paper has been greatly enhanced to engage with sources of a very high currency, and the manuscript demonstrates a sophisticated understanding of almost all concepts. The argument flows rationally and logically, with all claims that require citation or logical support being adequately supported. As I have noted in the manuscript, and briefly above, I believe addressing the recent challenges to Orch-Or would be very beneficial in making your argument clear, logical, and transparently grounded. Your comments on why you chose not to are logical, so you could incorporate those into the document. However, I believe some readers would want a more detailed analysis and engagement with some of the perceived or potential issues with the theory. Since it is such a major component of your argument and evidence, this should be approached in depth wherever possible.

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I don’t think there’s a misunderstanding at all except on your part: you’re doing metaphysical speculation and trying to make it look like science, but it’s pretty plain from the comments in this thread that you’re not doing science at all. The aspect that really gets me is that you have been giving as citations articles you haven’t even read – something that if I’d done on a science paper in university wouldn’t have just gotten me an F for the paper, it would have gotten me an F for the entire course. Another is that you keep talking about a theory but I don’t recall you ever putting forth a testable hypothesis based on that theory, let alone one that would distinguish your theory from existing views.

Here’s an idea: if you don’t have access to a source, DON’T USE IT.

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It doesn’t matter how many times you repeat that, it won’t magically become true.

Utter bollocks.

  1. You were lying about your sources long before you started using ChatGPT.

  2. ChatGPT’s output might include misquotes copied from secondary sources alongside a reference to the primary source, because that’s common practice among creationists, but it’s unlikely to accompany them with links and references to the original source when it’s different. Most creationists aren’t stupid enough to do that, so there’s nothing for ChatGPT to copy.

  3. If ChatGPT did somehow produce a misquote from a secondary source alongside a link to the original, you’d still be culpable for posting that text without checking that the quote was accurate.

  4. The original examples I have of you lying about your sources do not include any statement from you about using ChatGPT. So even if you were using ChatGPT at the time, you were still lying about your sources, by not mentioning that usage.

You have lied about your sources too often, for too long, in too many ways, for your latest excuses to be believed.

There is no reason for anyone to waste their time reading and commenting on ‘arguments’ generated by ChatGPT based on sources you admit you haven’t read and wouldn’t understand if you did.

Stop wasting people’s time with your incompetent garbage.

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I got this impression awhile back when the replies to my earlier comments were uncharacteristically short :laughing: