As Ayala (2007) explains, evolution by natural selection describes designs in nature without a designer.  For instance, when scientists use the term “random” to describe mutations, they refer to the unintentional nature of the process; mutations do not “attempt” to supply what the organism “needs” within a given moment or place. Instead, environmental factors influence only the rate not the course of mutation. For example, contact with harmful chemicals might increase mutation rates but will not increase beneficial mutations that make an organism resistant to those chemicals. In this sense, mutations are considered random because there is no “conscious” intent involved, which suggests there is no personal agent selecting adaptive combinations in evolution. He further explains how this description of mutations essentially forms the basis of the Modern Synthesis theory, which was proposed between 1936 and 1947 and reflects the consensus on how evolution proceeds. The expansion of 19th-century evolutionary ideas by Charles Darwin, Gregor Mendel, and others laboring on population genetics between 1918 and 1932 incentivized the Modern Synthesis theory, by showcasing that Mendelian genetics was consistent with natural selection and gradualism. 
Challenging new data are currently being produced in multiple fields and as a result, a different vision of evolution is beginning to manifest wherein the processes by which organisms develop are recognized as causes of evolution.  For instance, analysis of the genomes of 46 sequenced isolates of Escherichia coli provides a statistically supported comparison of the topologies of the phylogenetic trees for regulatory regions, their regulated genes, and the species tree. The results of this comparison strikingly show that evolution of the regulatory regions of over half of the core genes (i.e., genes shared by all isolates) was incongruent with that of the species tree. 
Moreover, “our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved.” 
Thus, new questions are raised in light of new evidence. Should evolution be considered a truly random process or a directed one? Do all living organisms share a common ancestor or a common mechanism?
The intelligent design (ID) theory much better agrees with new empirical evidence and can elegantly explain the abrupt origins we find throughout the fossil record and the incongruencies of species trees.
Based on previous studies and the literature, I aim to prove the existence of a universal common designer in nature by showing that there is a universal common design in evolution. Previous attempts to reintroduce an intelligent designer into science by ID theorists have failed for several reasons. ID theorists argue that the very presence of complex specified information (CSI) found in DNA automatically provides empirical support for the claim that an intelligent designer created and designed life because only human designers can produce CSI based on uniform experience. ID theorists attempt to provide more displays of irreducible complexity or specified information in nature to prove that an intelligent designer designed all living organisms. This involves showing how removing one part of a complex design, such as an eye, would cause the entire system to cease functioning. However, human designers are finite and fallible beings that design things based on limited prior knowledge by using and modifying preexisting material, which would merely mimic Neo-Darwinian mechanisms. More importantly, ID theorists have not yet attempted to prove or explore the nature of this designer.
Unlike ID theorists, Roger Penrose and Stuart Hammeroff have explored the nature of this intelligent designer, through a gravity-induced self-collapse, which they refer to as a “universal protoconsciouness.” They provide a comprehensive model of the nature and mechanism of this conscious agent that can explain the origin and evolution of life, species, and consciousness.  However, their theory does not go so far as to differentiate this conscious agent from mindless forces. For instance, even if the proposed experiments confirmed Penrose’s prediction, all it would prove is that non-biological settings are displaying elements that mirror conscious behavior. However, this would be considered as anthropomorphism.
The Modern Synthesis theory holds two key assumptions that are derived from the Extended Modern Synthesis theory : (1) mutations are a random process and (2) all living organisms have a common ancestor. This article considers both assumptions but primarily focuses on the latter. I will show how the mechanism of consciousness can explain and predict how biological processes developed over time on earth. Finally, I will provide a model describing the nature of this designer in more detail and further improve on the Orch-OR theory.
According to the Orch-OR theory, the action of consciousness proceeds in a way that cannot be described by algorithmic processes. Consciousness can contemplate or freely think about a plethora of ideas or information. Moreover, it can make judgements that one continually makes while in a conscious state. This involves distinguishing between true and false statements or what is morally right versus wrong.
The only thing in nature that does this is wave function collapse where you have a superposition of possibilities that collapses to one or the other. For example, the conscious observer must first specify or think of which wave-function he or she intends to measure and then, put in place a measuring device that will probe that aspect. The results of quantum physics experiments like “quantum erasure with casually disconnected choice” demonstrate this reality.
[2208.03726] Human Perception as a Phenomenon of Quantization (arxiv.org)
Furthermore, we have empirical support showing that the brain uses quantum mechanical processes, such as quantum tunneling and superposition, which would suggest more than correlation but causation is involved: For instance, researchers built an artificial cell-like environment with nano-scale engineering and repeated spontaneous growth of tubulin protein to its complex with and without electromagnetic signal.
They used “64 combinations of plant, animal and fungi tubulins and several doping molecules used as drugs and repeatedly observed that the long reported common frequency region where protein folds mechanically and its structures vibrate electromagnetically. Under pumping, the growth process exhibited a unique organized behavior unprecedented otherwise.”
Live visualizations of single isolated tubulin protein self-assembly via tunneling current: effect of electromagnetic pumping during spontaneous growth of microtubule | Scientific Reports (nature.com)
This means that we can use the action of consciousness as a mechanism that explains and predicts how biological processes developed over time on earth. In the next section, I am going to highlight observations that suggest a non-local consciousness exists in nature.
Objective Reduction Theory
The acceleration of the expansion of the universe from inflation is thought to be produced from an explosion or collision of quantum fluctuations of particles—called the “cosmological constant”—that permeate the entire multi-verse where a billion (plus one) positive particles and a billion negative particles come into existence at once. 
The cosmological constant is placed at a precise measurement of 10 to the 120th power. When scientists trace the rate of expansion back one second after the Planck scale of our universe, the value becomes an astounding 10 to the 10 to the 123rd power.
Hypothetically, this indicates that if our universe’s expansion rate had different values with larger amounts of dark energy, the universes created in the expansion that formed planets and stars, where life of any kind might evolve, would have most likely blown apart the cosmic material instead. If our universe’s expansion rate had different values with smaller amounts of dark energy, the universes created in the expansion would have most likely collapsed back into a singularity before it ever reached its present size.
This would suggest that Penrose’s mechanism of gravity-induced collapse is truly consciousness, and that this consciousness necessarily possesses non-computable traits, such as omnipotence. For instance, our multi-verse will most likely accelerate forever in all directions and produce an infinite number of pocket universes from the universal wave-function, according to the eternal inflationary theory. This would suggest that this “mind” not only exists in all possible configurations of matter but must exist in them by necessity.
This non-computable choice seems to play a role in biology as well. For instance, as Mattick and Dinger pointed, it has long been argued that the presence of non-protein coding or so-called ‘junk DNA’ that comprises > 90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, which would argue against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information. This objection has been essentially refuted in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms In fact, we now know that well over 80% of junk DNA is functional. It is noteworthy that there is controversy surrounding the ENCODE results (Eddy, 2012; Graur et al., 2013). I refer readers to this article that addresses and responds to objections.
The vast majority of mutations in regions that do encode proteins are deleterious and would prevent beneficial mutations from being fixated within the population. However, in a study on 34 E. coli strains, Martincorena, Seshasayee & Luscombe (2012) discovered that the mutation frequency varies across bacterial genomes. Some regional “hot spots” have a reasonably high mutation rate, while “cold spots” display a reasonably low rate of genetic changes. The researchers discovered that the hot- and cold-spot locations are not random (Martincorena et al., 2012). Thus, it appears that the mutation rates have been fine-tuned to lower the risk of harmful genetic changes (Martincorena et al., 2012; Martincorena & Luscombe, 2013). Recent studies seem to have converged on the same conclusion as well.
I am incorporating the following Penrose’s Objective-reduction (OR) theory in my model:
“In the Copenhagen interpretation, postcollapse states selected by conscious observation are chosen randomly, probabilistically (the Born rule, after physicist Max Born). However, in Penrose OR, the choices (and quality of subjective experience) are influenced by resonate with what Penrose called noncomputable Platonic values embedded in the fine scale structure of spacetime geometry”
In other words, whether a quantum system is displaying particle- or wave-like behavior depends on a non-computable conscious choice.
Universal protoconsciousness: universal self-collapsing wave-function
In the next section, I am going to highlight some experiments and observations that show how this protoconsciousness does not simply simulate human consciousness but posseseses a human personality.
Universal common designer
A recent prebiotic experiment demonstrated how self-replicating RNA molecules could “evolve into complex living systems by expanding their information and functions open-endedly.” More importantly, the similarity between logic gates and DNA structure and metabolism suggests that the characteristics of objects produced by human designers and biochemical systems are identical. 
Given the prior support for the Orch-OR theory, cosmological constant and non-random mutations, this universal protoconsciousness probably operated like humans when designing life on earth. This indicates that we would not have to prove or assume that some supernatural force/substance existed first to consider the existence of God as a potential explanation for a biological phenomenon because the evidence in quantum physics is compatible with panpsychism (i.e., a form of idealism).
More importantly, we need not consider using an unfalsifiable theory that involves an omnipotent human because a non-computable being cannot violate his own nature.
In other words, the non-computable trait this designer possesses offsets the omnipotent trait the designer would also have to possess. Therefore, we would expect God to be consistent with human nature without the flaws that humans naturally commit because of their inherent physical limitations.
This is what enables us to treat an omnipotent God the same way we would with other intelligent agents (Neanderthals, modern humans, aliens, etc.) when considering a valid cause to explain a biological phenomenon over a mindless force.
Thus, all candidates are considered natural but immaterial causes that we can test because consciousness is fundamental but not classical physics.
If this theory is true, we would expect all currently living organisms to have a common design that can be traced back to this universal common designer.
Universal common designer: universal self-collapsing wave-function
Universal Common Design Hypothesis
This non-computable conscious agent chose to re-use viruses and microtubules to develop created kinds of animals to survive, reproduce, and develop in different environments
Origin of life and species model
Around 3.8 billion years ago, billions of viroids, likely containing all the required genes to make certain evolutionary trajectories, were created within the deep-sea hypothermal vents of the Earth through self-collapse of the wave-function. Through natural selection and self-collapse, these groups of viroids evolved into different species of unicellular organisms, which underwent extensive horizontal regulatory gene transfer (HRT), leading to the formation of multicellular plants and fungi .
Subsequently, HRT and microtubules to develop cell differentiation, sexual reproduction, and consciousness into the first group of marine basic types (fish, marine invertebrates, amphibians).
Then, reptiles, birds, and mammals were later developed from different times and global locations within the earth.
(A) We would expect similar phenotypic traits to evolve separately in nested but unrelated taxa in response to similar needs.
(B) We expect to find functional ERV’s and pseudogenes in nested but unrelated taxa
(C) We would expect to find that the phylogenetic trees for regulatory regions in nested but unrelated taxa to better fit the data than species trees.
(D) We expect to find adaptive convergent genes in genomes between nested but unrelated taxa
(F) We would NOT expect to find examples of non-human animals displaying forms of human exceptionalism, such as:
Ability to invent and use grammar, verb tenses, and vocabulary up to hundreds of thousands of words
Ability to invent and use complex trading and transportation systems like modern humans
Ability to engage in mathematics, literature, philosophy, and theology
Ability to tame, domesticate, and train mammals, birds, and small lizards
We can test prediction (A) by first showing how shared traits, such as vestigial structures, have functional utility. Then, we apply those same traits between nested groups to different environmental niches. This method was used in the study of the red and giant pandas that concluded they were unrelated.
As a test run, we will evaluate Equidae to determine whether they are a basic type, drawing on data from the extensive work that has been previously done. For instance, it has been shown that all horses are of a single basic type. Most importantly, based on preliminary results, we found evidence that horses were, for the most part, sufficiently different from tapirs and rhinos, which belong to separate taxonomic groups.
The results from the preliminary test are shown below:
Are the common features of this group being used differently?
(A) Habitat? TBD
(B) Food? No
(C) Reproduction? No
(C) Predators? Yes
It is reported that “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."
Scholars have stated that “tapirs are strong swimmers who may walk along the bottom of river beds 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 back let go.” [just ask for references]
Horses, tapirs, and rhinos all have odd numbers of toes, which they use differently pertaining to their habitats and predators; horses run from predators in open terrain, tapirs swim to avoid predators in the water, and rhinos charge predators. Therefore, we can conclude that Equidae is a legitimate basic type that shares a common design with tapirs and rhinos, based on these lines of evidence:
Fossil dissimilarities between Equidae and other Perissodactyls.
A clear-cut fossil lineage within the Equidae family.
The odd toe evolved separately in response to similar needs.
However, this conclusion is tentative because new research, with a greater sampling of non-equid outgroups, is still required to test the hypothesis that all equids form a single holobaramin or a basic type…