Universal Common Design theory
This common designer implies having a common design rather than a common descent because only humans produce top-down causation in the form of algorithmic information or RNA viruses. More importantly, observations have suggested that viruses were not only the probable precursors of the first cells but also helped shape and build the genomes of all species, including humans. [36]
For instance, scientists synthesized the RNA molecules of a virus and reconstructed a virus particle from scratch. [37] They accomplished this by creating another virus and using its parts, such as specialized proteins (enzymes), to construct an RNA virus to solve the problem of an unstable RNA. Other experiments have shown that RNA viruses can be engineered to interact with the host miRNA pathways, and miRNAs can be used to control viral tropism. [38]
For example, endogenous retroviruses (ERVs) protect the host cell’s genome from retroviral infections by disrupting the endogenization process of invading retroviruses. ERVs must resemble retroviruses to act as a defense mechanism against incoming harmful viruses. [39]
A different study from Kazuaki Monde et al. also revealed that “the strict dependence of HERV-K on SOX-2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos.” [40]
This is how human designers operate. They use preexisting mechanisms, material parts, and digital information to assemble designs to achieve a purpose.
The other reason a common designer implies having a common design rather than a common descent is because natural selection lacks the capacity to elucidate the physical mechanisms underlying the transition from non-life to life or to distinguish non-living from living. [41]
Furthermore, RNA viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic—they have many evolutionary origins. [42]
Overall, this is why we can infer that all living animals share a common design that can be traced back to a universal common designer. If this theory is true, then we can expect humans to possess cognitive qualities that are exceptions to what would otherwise be predicted if we were evolutionary descendants, such as
KIF18a [also known as (a.k.a.) Kinesin 8]
KNL1 (a.k.a. CASC5)
SPAG5 (a.k.a. astrin)
Endorestiform Nucleus
These examples involve the cognitive abilities of the human brain that either have not been observed to be present in animal brains or do not work properly in animal brains through experimentation.
Definitions
Common design: To create and develop animals through the common process of HRT for the common purpose of surviving, reproducing, and pioneering different environments.
Universal common designer: universal self-collapsing genetic code shown by the shared DNA among all living organisms (i.e., objective reduction).
Created kinds: A recognizable base form and structure that does not change over time (Breeds within a kind). They are separate, unique (no common ancestors), and fully functional (no trial and error). Similar in form/design/ variable surface features owing to the similarity in function and common designer. It can produce many species, has wide genetic diversity, and can acclimate to the environment. [43] Example: 196 Bird kinds, Wolf kind, Elephant Kind.
Species: A similar base form and similar surface features that do change over time, such as size and color (breeds within a species). Represents the entire group related by common ancestry from present generations. It can produce many varieties, has narrow genetic diversity, and is acclimated to the environment. [43] Example: over 10,000 bird species today; Wolf/Dog/Fox; Asian and African elephants/Mastodon/Mammoth.
Basic types: Represents the entire group related by common ancestry, including both past (created kinds) and present generations (species). The reproductive discontinuity between basic types; reproductive continuity within a basic type.
Wood [44] provides a list of taxa from the common descent model that is considered “basic types” or “species” according to the common design model.
Origin of life and species model
Approximately 3.8 billion years ago, pi electron resonance clouds in single-chain amphiphile molecules coalesced in geometric pi-stacks, forming viroids with quantum-friendly regions for OR events within Earth’s deep-sea hypothermal vents. [45]
Subsequently, through natural selection and OR events, groups of viroids formed into highly ordered local domains of key biomolecules of a DNA/RNA virus or molecule, which later evolved into different species of unicellular organisms. [46]
Through HRT, these unicellular organisms underwent extensive regulatory switching and rewiring in their noncoding regulatory regions, which led to the divergence of transcription start sites and gene expression levels in the formation of primitive multicellular organisms. This same multicellular toolkit and modules of slime molds then developed into created kinds at different times and global locations (for more details, read Stuart Hammeroff’s description of how microtubules played a part in the origin of species). [5]
This model already has a history of accurate predictions regarding gaps in the fossil record. For instance, the fossil record has revealed that the observed pattern of no evolutionary change punctuated by rapid biological innovations matches the patterns predicted [47] if a common design/archetype accounts for life’s history and diversity.
For instance, God fine-tuned life in just-right forms, at just-right times, and at just-right abundance and diversity levels and replaced those life forms via mass extinction events followed quickly by mass speciation events. The new life forms removed the just-right amounts of carbon dioxide and methane from the atmosphere to perfectly compensate for the brightening Sun. [48]
Without a conscious mind, there would be no possibility of perfectly compensating for the increasing brightness of the Sun so that life can be continuously sustained on Earth throughout the past 3.8 billion years.
This activity would explain how instances of high gene-tree conflict (discordance in phylogenetic signals across genes) in mammals, birds, and several major plant clades correspond to increased rates of morphological innovation. [49]
Origin of species predictions
Based on this theory, we would expect to find:
(A) Over 80% of families and orders evolved separately.
(B) Over 80% of ERVs and pseudogenes are functional.
(C) The regulatory regions of core gene promoters between families and orders are over 80% incongruent with species phylogenies (i.e., vertical inheritance).
See the list of suspected basic types based on preliminary analysis. [44] In addition, read Appendix 2 for an explanation of why these predictions are separate from the common descent model.
Methods
We can assess prediction (A) by applying analogous phenotypic traits between families and orders to different environmental niches based on similar needs.
There is a four-question survey where each practical criterion is designated by a letter (A–D) and a title in the form of a question (relating to food, predators, reproduction, and habitat).
For example, if the answer to the question “Is the common feature of this group being used differently in their habitats?” is “No,” “To be determined (TBD)," or “Not applicable (N/A),” a follow-up question is asked: “Do they respond differently in different habitats?” This may require artificially planting them in different habitats for an answer. If the answer to either question is “Yes,” we can start testing whether there are adaptive and structural convergent genes pertaining to the application of this analogous trait. If the test reveals at least one adaptive and/or structural gene, we can confidently conclude a common design.
However, if the answer to both questions is “No” or “TBD,” we must apply the same question formula to prey and/or predator measures to potentially draw a definite conclusion. If the answer is still “No” or “TBD,” then we ask, “Is the common feature of this group being used differently in sexual reproduction?”
The results are inconclusive if every question yields a “No” or “TBD” answer. This method was inspired by a study on red and giant pandas, which concluded that their false thumbs evolved separately in response to similar needs, [50] and a study that showed why and how they evolved separately. [51]
As a test run, we will evaluate the family Equidae to determine whether they are a “basic type,” by using the extensive work that has been done already. For instance, a recent study [52] confirmed the results of earlier studies, showing that all horses are of a single basic type. Most importantly, preliminary results showed evidence that horses were, for the most part, sufficiently different from tapirs and rhinos, which share the trait of odd numbers of toes. [53] However, these two studies mainly give us a good reason to “suspect” all three groups are basic types rather than only one group.
Results
Is the common feature of this group being used differently?
(A) Habitat? Yes
(B) Food? TBD
(C) Reproduction? N/A
(D) Predators? Yes
Horse behavior is best understood from the view that horses are prey animals with a well-developed fight-or-flight response. Their first reaction to a threat is often to flee, although sometimes they stand their ground and defend themselves or their offspring in cases where flight is untenable, such as when a foal is threatened. [54]
Tapirs are strong swimmers who may walk along the bottom of riverbeds to find food. They instinctively escape predation by moving into the water, and they can stay submerged in deep water long enough to make any predators clinging to their backs let go. [55]
Discussion
According to the ecological study, horses, tapirs, and rhinos use their odd toes differently, pertaining to their habitats and predators. Horses use this trait to run from predators in open terrain, tapirs use it for swimming and avoiding predators in the water, and rhinos use it to charge predators.
Future Research
Preliminary results suggest that Equidae is a legitimate basic type that shares a common design with tapir and rhino based on the odd-toed trait fitting different applications in response to similar needs.
However, this conclusion is tentative because we still need to find evidence for adaptive and structural convergent genes of the odd-toed trait. Future experiments should elucidate these underlying mechanisms and genes. The question that remains is:
“Should evolution be considered a truly random process or a directed one?” and “Do all living organisms share a common ancestor or a common mechanism?”
The common design model views convergence as resulting from a universal common designer who employs a single, optimal solution to address a common set of problems faced by organisms possessing different characteristics and living in different habitats.
Common descent views convergence as occurring when unrelated species encounter identical, or nearly identical, environmental, predatory, and/or competitive selection effects. In other words, common descent suggests that natural selection channels randomly occurring variations in unrelated species toward identical outcomes.
There are two obvious problems with the common descent explanation for convergence. First is the frequency with which it is observed to occur. For instance, a study by biologists demonstrated, at the molecular level, that evolution is both unpredictable and irreversible. [56] The study focused exclusively on the type of evolution known as purifying selection, which favors mutations with no or only a small effect in a fixed environment. This is in contrast to adaptation, in which mutations are selected if they increase an organism’s fitness in a new environment. Purifying selection is by far the more common type of selection.
Consequently, we would expect functional ERVs and pseudogenes to be extremely rare under common descent models. Second, occurrences of convergence where the environmental, predatory, and competitive selection effects would not at all be similar.
In contrast, the common design model predicts that over 80% of taxonomical groups have functional ERVs and pseudogenes because the mechanism the designer uses in the form of HRT naturally produces this effect, unlike natural selection (See the competitive endogenous RNA (ceRNA) hypothesis). [57]
For further research, evolutionary biologists, paleontologists, ecologists, and molecular biologist will need to look for morpho-molecular dissimilarities and/or lack of fossil intermediates among order and family level taxa. Then, they need to use the two-step ecology criteria described above to confidently conclude common design. Moreover, phylogeneticists will need to use bayisesan inferences to find out whether the common design model better fits the data than common descent when it is applied to the list of suspected created kinds and basic types.
Finally, it has been repeatedly found that what initially seemed to be non-functional ERV’s and psuedogenes caused by an unguided process turned out to be functional afterall with increasing understanding of the design [59]. Because a greater understanding revealed that these apparent vestigials still have function at various instances, further research may reveal how many other ERV’s and psuedogenes may actually be functional as well in future.
This type of research should answer these relevant questions and contribute to my theory, such as …
Origin of life: Exactly how, where, and when did life on Earth originate? What were the metabolic pathways used by the earliest life forms?
Origins of viruses: Exactly how and when did different groups of viruses originate?
Last Universal Common Ancestor: What were the characteristics of the Last Universal Common Ancestor of Archaea, Bacteria, and Eukaryotes? Did Archaea and Eukaryotes evolve out of the domain Bacteria or to a clade basal to it? Do Archaea and Eukaryotes share a later or earlier common ancestor to Bacteria?
All that is for the future. I can only say that the possible involvement of a universal common designer in genetic information processing has provided a novel way of analysing these processes.
Theoretical Difficulties
According to the universal common designer theory, God is omniscient and designed animals for the purpose of surviving, reproducing, and/or adapting. For this reason, God cannot design animals with features that hinder or reduce the probability of surviving, reproducing, and/or adapting.
However, there are currently some examples in nature that seem to conflict with the theory, such as the serum response factor, which causes heart failure in humans. In addition, humans cannot breathe and swallow at the same time due to our lowered voice box, which supposedly allows us to create a wider range of sounds.
In the future, we expect to find a sensible purpose for these alleged design flaws, showing that they do not reduce the probability of survival, reproduction, and adaptation but rather increase it.
For example, random bumps along the leading edge of the humpback’s fins seemed to hinder the aquadynamic efficiency of the humpback whale. However, Van Nierop et al. (2008) assembled a detailed model of the humpback whale fin and tested it in a wind tunnel. Their experiments demonstrated two things: first, the bumps are not as big a limiting factor in the whale’s straight-ahead swimming speed as was initially presumed, and second—and more unexpectedly—the bumps provided a major payoff for the whale in maneuverability. The bumps allow the whale to reach a much higher attack angle without losing essential momentum. [57]
Furthermore, God is omnibenevolent and designed animals for the purpose of surviving, reproducing, and/or adapting. For this reason, God will not design animals with pathogens or features that reduce the population or another animal’s ability to survive, reproduce, and fit an environmental niche.
However, there are current examples in nature that seem to conflict with the theory, such as
(i) Toxoplasma gondii and toxoplasmosis
(ii) Excretory or digestive systems of parasitic insects
(iii) Tongue-eating louse (a parasitic isopod)
(iv) Carnivorous behavioral genes of parasitic vertebrates
(v) The enzyme B-1 4 glucanase
In the future, we expect to find a sensible purpose for alleged “evil” designs that show they do not reduce (but increase) the population or another animal’s ability to survive, reproduce, and fit an environmental niche.
For example, in animals, injury can lead to long-lasting distress, whereby frequent exposure to pain-producing stimuli causes a progressively amplified response well after the injury has healed. This phenomenon has been referred to as “nociceptive sensitization.” Biomedical researchers have long viewed nociceptive sensitization as maladaptive because, in humans, it is associated with anxiety. [58]
However, Crook et al. (2014) studied nociceptive sensitizations in squids and concluded that heightened sensitivity to pain helps these creatures evade predation. Squids are an outstanding laboratory model because they undertake a precise sequence of defensive behaviors when threatened by a predator. When endangered, squids that fully recovered from a previous injury reacted sooner than those that had not been injured. Conversely, the previously injured squids exhibited a slower response to predatory threats when the scientists used anesthetic to block the pain immediately after injury, thus preventing nociceptive sensitization. As nociceptive sensitization is pervasive, it likely serves a similar benefit to other animals. Thus, these results indicate that pain (or suffering) plays a key role in enhancing the survival of animals following an injury and recovery.
Examples of design decay or design trade-offs in nature do not conflict with the theory. For instance, God cannot create a universe without decaying effects because the second law of thermodynamics is a feature of quantum mechanics; thus, it must exist in all possible worlds, unlike other laws of nature. [59] Design trade-offs we find in nature are also subject to the law of entropy. For this reason, God would not be held responsible for a genuine design flaw or cruel design feature under these circumstances.
In the future, it will be paramount for scientists to reexamine the remaining claims of design flaws by looking at the organism as a whole, even if it exhibits some features that may be perplexing, rather than make an argument from ignorance or personal incredulity. By encouraging researchers to look at the overall design and purpose of an organism as well as expand and test different taxonomical groups, the aim is to accelerate scientific discoveries and provide more support for this explanatory model.
Appendix
According to the laws of logic, [60] the attributes of God have to work in accordance with each other in a logically consistent manner because God is who God is (i.e., the law of identity) and cannot simultaneously not be who God is (i.e., the law of non-contradiction).
This means that God cannot make God cease to exist because this would conflict with God being a necessary being. God cannot make a square circle because this would conflict with God’s omniscience. God cannot lie because it would conflict with God’s omnibenevolence. God cannot make a rock so heavy that God cannot lift it because it would conflict with God’s omnipotence.
Most importantly, God cannot create and develop a world that does not have God intimately involved in the process every step of the way because it would conflict with God’s “personal” nature. Thus, God must be true to “all” God’s attributes because to do otherwise would be to deny God’s own self.
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