A Comprehensive Theory of Intelligent Design

INTRODUCTION

Previously, I argued that we can test whether a Universal common designer exists in biochemistry to explain the origin of digital information. What I mean by “Universal” is existing by necessity where a natural world with life could not possibly have been otherwise without an intelligence. What I mean by “common designer” is a human mind that is composed of digital information and consciousness according to Orch-OR’s theory of consciousness (Hameroff, Stuart; Penrose, Roger 2014). Both combined make a Universal mind.

I, initially, made this inference based on the experiment done by Church and Kosuri (2012), which suggested that how the similarity between digital information in DNA and human language was more than just metaphorical but literal. For instance, they created a biotech version of an e-reader, with the highest storage capacity to date. This involved encoding an entire book (along with illustrations) in DNA. The book consisted of 53,246 words, 11 JPG images, and even a javascript program.

More importantly, I made this inference based on in-vitro selection experiments, which suggested that intelligence was required for life to emerge. For example, whenever unguided chemical processes under atmospheric conditions were left to themselves without any interference, they did not produce the desired results. Rather, the living state would always subside and turn into “useless networks of RNA sequences” as demonstrated by Szostak and Bartel (1993) where more than half of the pool of RNA molecules precipitated when incubated. They were able to solve this problem by tying the molecules onto a substrate to make sure the pool of RNA molecules do not diffuse and form intermolecular reactions, and, thus, safely incubated. Although this is an unlikely occurrence within the primordial soup, this was the prevailing inclination within in vitro selection experiments under atmospheric conditions (Breaker & Joyce 1994). So the question now becomes…

What if all currently living organisms have a common design from a universal common designer rather than a universal common descent from a universal common ancestor?

it is important to note that this theory will be an improvement of the Modern Synthesis NOT a negation, but it will not offer an explanation for how consciousness arose either. Lastly, I will be showing how the origin of our life and advanced life emerged this time unlike the previous topic I created:

Possible experiment to test for a “Divine” intelligent designer - Peaceful Science

UNIVERSAL COMMON DESIGN THEORY

A Universal common designer formed the first life and the anatomical structures of multicellular life separately from the physical-chemical world and continues to maintain these structures by ensuring that the organism’s distinctive shape, control, arrangement of body parts, DNA, etc. generate traits that fit the environments it occupies to survive, reproduce, and fill the biosphere.

This means that the functional systems as a whole between organisms and how you compare these fully functional systems between organisms to their respective environments would provide a very key difference and separation from common ancestry’s predictions.

For example, contrary to what evolutionists have previously expressed about the "bad design, " of the giant panda’s thumb, A study analyzed it and showed that the radial sesamoid bone (its “thumb”) is “one of the most extraordinary manipulation systems” among mammals. Following this publication, another study found that the giant panda and the red panda were not related even though both species possess the false thumb. The false thumb of the giant panda was intended to manipulate bamboo and the false thumb of the red panda was designed as an aid for arboreal locomotion, With the red panda secondarily developing its ability for item manipulation.

(A) Design Decay hypothesis

There are three main hypothesizes on the origin of viruses with no clear explanation as to which one is correct:

  1. The virus-first hypothesis claims that viruses predate or coevolved with their current cellular hosts; 2. The progressive, or escape, hypothesis claims that viruses arose from genetic elements that gained the ability to move between cells; 3. the regressive, or reduction, hypothesis suggests that viruses are remnants of cellular organisms (Wessner, David R. 2010).

However, what if all three hypotheses are true?

For instance, viruses are responsible for the abatement of 80% of prokaryotic heterotrophic production. Virus-induced prokaryotic mortality rises with increasing water depth, and beneath a depth of 1,000 m almost all of the prokaryotic heterotrophic production is converted into organic detritus. The viral shunt, releasing on a global scale ~0.37–0.63 gigaton of carbon per year, is a vital source of labile organic detritus in the deep-sea ecosystems. This process sustains a high prokaryotic biomass has a significant influence on prokaryotic metabolism, allowing the system to manage the severe organic resource limitation of deep-sea ecosystems and seems to play a vital role in global biogeochemical cycles (Danovaro et al., 2008).

The beneficial role of viruses applies to terrestrial environments as well since viruses modulate host population ecology, food web structure, energy and nutrient flow between habitats, and apparent competition processes, and they favor habitat formation and can transfer genetic information (Lefèvre et al., 2009; Wessner, 2010).

More importantly, researchers from the University of Connecticut discovered through modeling studies that horizontal gene transfer among microbes has the same genetic signature as common ancestry. Horizontal gene transfer encompasses any mechanism that transfers genetic material to another organism without the recipient being the offspring of the donor.

According to all these studies, the systems would have similar functions and have similar parts used to construct species, but it is the specified complexity of the shapes, arrangements, and DNA that allows organisms to fit specific applications which gives them their separate uniqueness. This would explain why and how humans share the appearance of universal common ancestry, such as viruses being used to initiate design diversity around the globe.

How to determine whether evolution was a completely guided process?

(A) Experiments

When the biologist chooses a particular set of natural conditions to work on from using a Lenski type experiment, the observer has to first test and determine whether or not life can be developed within that condition without interference. Then, the observer must perform the same experiment with the same set of natural conditions following the previous one but impose unrealistic interference in the second round of experiments.

The combined outcomes of these experiments would produce evidence for the hypothesis. If we apply the same procedure to a different natural condition, it would produce additional evidence for this hypothesis. This is because even though the experimenter who guides evolution within each natural condition is finite and contingent, there could not be any conscious life before simple life emerged, hence why we have to include the first experiment to support the “necessary” attribute of this common designer.

For example, phage-assisted continuous evolution (with the apt acronym “PACE”) is a microbial experiment where molecules from E.coli drift through a provocatively named “lagoon” filled with bacteriophages. Each phage contains a copy of the gene of interest (GOI) that will undergo directed evolution. To successfully infect E. coli, the phage requires a protein called pIII (Badran & Liu, 2015). To force the GOI to evolve, researchers substitute the phage gene for pIII into the bacteria, linking its expression to the activity of the GOI. Thus, phage containing more active versions of the GOI will generate more pIII and will be more infectious, spreading more copies of that version of the GOI as they infect more hosts. Eventually, only the most successful mutant version(s) of the GOI will be left. However, the phages that are lacking the functional pIII protein are rapidly lost under continuous culture conditions because they have no ability to propagate (Badran & Liu, 2015).

Therefore, the fundamental difference between Lenski’s experiment and this directed evolution experiment is that the experimenter intervenes within the material process of natural selection and random mutations and inserts specialized proteins within the organism to give it a boost in function and fitness. This is considered unnatural because a random view of mutations has not been shown to produce either novel gains or consistent gains in nature or in the laboratory. Especially, when viruses have only been shown to arise without a host from scientists who genetically or synthetically create viruses (Smith et al., 2003)

However, if, at some point, someone produces new information from these viruses within a natural condition that does not require a conscious agent, then this would falsify the common design theory completely.

(B) Observations

Although previous studies seem to suggest that life must be directed by a Divine intelligence, critics have pointed out apparent flaws within this design inference. In his book Why Evolution is True, evolutionary biologist Coyne claims, “Imperfect design is the mark of evolution; in fact it’s precisely what we expect from evolution.” (Coyne, 2014, p. 81)

His prediction is based upon the observation that “[n]ew parts don’t evolve from old ones, and we have to work well with the parts that have already evolved. Because of this, we should expect compromises: some features that work pretty well, but some not as well as they might, or some features—like the kiwi wing—that don’t work at all, but are evolutionary leftovers.” (Coyne, 2014, p. 81)

Coyne is not the first to make this argument. In the mostly anti-ID volume Intelligent Design Creationism and its Critics, Smith states, “if a design in nature is clearly inferior to what a human engineer could produce, then we are entitled to [reject ID]” (Smith, 2001, p. 724).

The examples of supposed design flaws come in four forms. The first form encompasses suboptimal designs, which are optimized for their purpose but not completely optimized to exercise their full potential in achieving that purpose when compared to similar designs that show better optimization. The second form comprises bad designs, which are considered poorly made to achieve their recognized purpose. The fundamental difference between a bad and a suboptimal design is that bad designs are designs considered not constructed well, while suboptimal designs are those considered not constructed well enough. The third form includes useless designs; designs without function, which probably had function in the past. Finally, the fourth form comprises sinister designs, in which organisms are designed in a way that seem to only bring harm and degeneration upon that organism or to other organisms.

However, upon further inspection, it has been repeatedly found that what initially seemed to be design flaws caused by an unguided process instead of a divine agent turned out not to be flaws at all with increasing understanding of the design (just ask for the list). In 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.

Theoretical Difficulties

What looks like a flaw from the harmful effects of cancerous mutations in organisms is primarily a result of decay imposed by the second law of thermodynamics rather than poor design (Serena Nik-Zainal and Benjamin A. Hall, 2019). However, some might argue that an all-powerful all-knowing omnibenevolent common designer, whose purpose is to ensure species survive and reproduce under natural conditions, could have effectively designed living organisms in which these flaws would not occur at all. However, the second law of thermodynamics must exist in all possible worlds unlike other laws of nature because it pertains to quantum mechanics as well as general relativity (Abe & Okuyama, 2011). This means it would require the suspension of the second law (i.e., a miracle) to prevent them from occurring at all.

According to the theory, we would not expect a miracle or random event to happen based upon that designer’s personal nature that is similar to ours. More importantly, it appears as though this designer uses the laws of nature to eliminate these instances and chooses to remain consistent with them. This involves editing and limiting the harmful genetic changes (Martincorena et al., 2012; Martincorena & Luscombe, 2013; Garvin & Gharrett, 2014) 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 (Moore et al., 2010; Smee, 2012; Gilljam, 2015).

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.

In addition, there are examples of cancer cells developing through viral infection (Morelli et al., 2004) and thus, as stated before, viruses are necessary evils. Further research might find more cases like these in other genetic diseases.

With that said, these explanations do not adequately explain why we see these occurrences in humans since we seem to be uniquely made in the image of this designer where we have the ability to recognize and manipulate digital information to our advantage, which we don’t definitively see in animals yet. For this reason, we would most likely expect this designer to want a special relationship with humans based on human experience.

Look, none of that makes any sense. It’s word salad. If you have anything reasonable to say there you aren’t communicating it in clear language. No purpose is served by the word “universal”. Saying that the designer is a human mind is confusing, as you clearly don’t intend that the designer is human. “Orch-OR” is an obscure term. And why is the information in life necessarily digital? Etc.

No, it didn’t. Sure, you can encode human language in DNA. But that doesn’t make it language. And because you can represent DNA sequences digitally doesn’t make that information digital either.

But they don’t. Isn’t this just a reposting of your previous claims, unmodified in response to any of the criticisms?

Then we don’t expect nested hierarchy, unless you aren’t really contrasting design with common ancestry. Hard to know whether you meant to say what you said or imply what you implied.

Does it? Why? And you never say what the difference is. It isn’t clear what your example is supposed to show.

At this point I stopped reading, since you lose all connection to any thread of argument.

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I specifically said ,at the end, that both definitions combine to make a Universal mind, which would be a quantum mind that is not contingent upon classical space-time physics or a prior cause and is the first cause from which all organisms now living on Earth have a common design or blueprint originating from this designer, which would be digital information.

I was merely referencing where I got my definition of a human mind from.

I am not sure what you are getting at here. I never suggested this. The information in life is both analog and digital.

I need you to be more clear here. What makes you say that? Please elaborate so I can respond adequately.

NO, I did modify and made the necessary changes after you guys made your critiques and even put you on notice. But, I did not see any meaningful responses on my latest changes so I decided to just move on and make this topic.

Correct, there is not supposed to be a big contrast between common design and descent. Common ancestry is still pervasive in this model just not “Universal”. This is why I did not feel compelled to go into detail in regards to the model . However, I can’t tell you exactly which species were designed separately, especially when science does not provide a clear definition of “species” and the bible does not provide a clear definition of “kinds”. It is just something that we will have to find out later through testing of this model in regards to which organisms were designed separately and reclassify them from that point on

No, I did. You just stopped reading at that point, Silly Billy. Here it is again…

According to all these studies, the systems would have similar functions and have similar parts used to construct species, but it is the specified complexity of the shapes, arrangements, and DNA that allows organisms to fit specific applications which gives them their separate uniqueness. This would explain why and how humans share the appearance of universal common ancestry, such as viruses being used to initiate design diversity around the globe.

Thanks to John Harshman! Saves time!

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Everything you type seems like gibberish to me. There are two possibilities: 1) Your thinking is as muddled as it appears; 2) Your thinking is fine, but you are so poor at communicating that it’s impossible to tell what you’re trying to say. I don’t see a third.

The fact that you can’t tell the difference between ancestry and separate creation should be instructive for you.

Shouldn’t “kinds” be obvious to inspection if they really existed?

How would you test that?

No, it explains nothing. It’s just a sentence assembled from random buzzwords.

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NO, I can tell the difference based on the available evidence within the fossil record and scripture and I just tell you to the extent that you are suggesting.

Read the rest of my article to find out.

Say what?

I read it, but it doesn’t say anything about “kinds”, and your test is nonsensical. Your conception of your own brilliance needs deflation.

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Again, the functional systems between organisms as a whole and how you compare these fully functional systems between organisms to their respective environments are two key differences that separate it from common ancestry’s predictions.

For example, a study analyzed it and showed that the radial sesamoid bone (its “thumb”) is “one of the most extraordinary manipulation systems” among mammals. Following this publication, another study found that the giant panda and the red panda were not related even though both species possess the false thumb. The false thumb of the giant panda was intended to manipulate bamboo and the false thumb of the red panda was designed as an aid for arboreal locomotion, With the red panda secondarily developing its ability for item manipulation.

As you can see, the systems have similar functions and have similar parts used to construct species, such as viruses, but it is the system as a whole ranging from the shapes, arrangements, and DNA that allows organisms to fit specific applications in nature, which gives them their separate uniqueness.

What else is there to explain and understand?

Then, please do the honors of deflating my ego and show me how my test is nonsensical.

How that little story has anything to do with distinguishing design from common descent. Either your communication skills are not good enough to express your ideas or your ideas are nonsense. Or it could be both.

Hard to do, since it’s impossible to tell what your test is actually supposed to do.

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Simple. The test was there to distinguish design from common descent. According to descent, we would expect there to be design flaws while under a common design model we would expect there to be NO design flaws. I already gave examples of what has been deemed a design flaw according to a divine design model at the start of this topic.

The other test involved showing how a divine intelligence was the primary cause for evolution rather than the environment.

The only examples of conscious design we have observed are those of humans and other relatively intelligent organisms. Guess what? Those designs are sometimes flawed, so your hypothesis test is practically useless. Of course, you might argue you mean “divine” design, but neither you, me or anyone else has observed anything like that, so you can’t tell whether divine design can be flawed or not.

If I played along though its darn obvious common descent wins. We have a GULO pseudogene, which is unable to help make vitamin C. Under a common conscious design framework that’s an unbelievably stupid design flaw. Under common descent, if an ancestral population lost the function of a gene due to mutations, and that defunct gene is passed on, we expect to see a fairly consistent distribution pattern for that defunct gene in extant descendants. Guess what again? That’s what we see for the GULO pseudogene, among primates including us, for example.

Continuously spewing junk like this will make others easily lose interest in the things you say.

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I’m sorry. There’s nothing we can discuss.

I beg to differ. We can tell. According to the theory, we would expect this divine designer to be all-powerful, all-knowing, and all-loving, which means we would not expect to see any design flaws.

The examples of supposed design flaws come in four forms. The first form encompasses suboptimal designs, which are optimized for their purpose but not completely optimized to exercise their full potential in achieving that purpose when compared to similar designs that show better optimization. The second form comprises bad designs, which are considered poorly made to achieve their recognized purpose.

The fundamental difference between a bad and a suboptimal design is that bad designs are designs considered not constructed well, while suboptimal designs are those considered not constructed well enough. The third form includes useless designs; designs without function, which probably had function in the past. Finally, the fourth form comprises sinister designs, in which organisms are designed in a way that seem to only bring harm and degeneration upon that organism or to other organisms.

However, upon further inspection, it has been repeatedly found that what initially seemed to be design flaws caused by an unguided process instead of a divine agent turned out not to be flaws at all with increasing understanding of the design (just ask for the list). In 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. This would confirm the theory each time we find another alleged design flaw to be optimal. This leads me to the next thing you said…

The researchers concluded in the study I referenced below: “transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression.”

  1. Shanker Kalyana-Sundaram et al., “Expressed Pseudogenes in the Transcriptional Landscape of Human Cancers,” Cell 149 (June 22, 2012): 1622–34.

This reminds me of a movie title, and the accompanying synopsis, in the Philadelphia Inquirer. The listing was for the film “Frankenstein Must Be Destroyed.” The synopsis was: “Yeah. You do it.”

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There are design flaws in biological systems and one that sorely sticks out is the GULO pseudogene. That pseudogene horrendously falsifies your useless hypothesis.

The GULO pseudogene falls into the third and fourth categories.

We have a good understanding of the GULO pseudogene (GULOP). We also know that the inaction of GULOP has led to the death and suffering of millions of people who cannot access vitamin C in their diet.

That’s a terrible design flaw.

The effects of having a GULOP are pretty obvious. In fact, when we knock out functional version of GULO in mice, they end up with scurvy, and have to be rescued by dietary supplementation with vitamin C just like us. Again its a terrible design flaw.

This paper is of no relevance to GULOP whose nonfunctionality within the context of vitamin C biosynthesis has been empirically demonstrated using laboratory and clinical data.

GULOP is a design flaw and it falsifies your hypothesis.

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Did the paper address ALL psuedogenes? If not, what proportion of pseudogenes are transcribed?

Why are you citing a paper about cancer when you started out talking about life?

Why are you copy/pasting quotes instead of citing evidence?

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Yeah. Even if GULOP serves some other function, the absence of a functioning GULO gene in humans is bad design. (Unless, of course, scurvy is part of the design. As certain ID proponents tell us, we can’t presume to know the goals of the inscrutable Designer.)

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Well, of course most of the human genome is transcribed occasionally. That’s why mere transcription is not good evidence of function. There’s a lot of spurious transcription. You have to go much farther than that to demonstrate function.

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For future reference, when quoting verbatim or heavily from abstracts or other sources in general, it’s good practice to indicate the quotes and cite the source. You sometimes do the latter, but often fail to do the former.

4 examples from your OP:

1

Strongly paraphrasing from:

Thus, it seems that, whereas the false thumb of the giant panda probably evolved for manipulating bamboo, the false thumbs of the red panda and of S. batalleri more likely evolved as an aid for arboreal locomotion, with the red panda secondarily developing its ability for item manipulation and thus producing one of the most dramatic cases of convergence among vertebrates.

2

Copied almost verbatim from from the abstract:

Here we report that viral production in deep-sea benthic ecosystems worldwide is extremely high, and that viral infections are responsible for the abatement of 80% of prokaryotic heterotrophic production. Virus-induced prokaryotic mortality increases with increasing water depth, and beneath a depth of 1,000 m nearly all of the prokaryotic heterotrophic production is transformed into organic detritus. The viral shunt, releasing on a global scale approximately 0.37-0.63 gigatonnes of carbon per year, is an essential source of labile organic detritus in the deep-sea ecosystems. This process sustains a high prokaryotic biomass and provides an important contribution to prokaryotic metabolism, allowing the system to cope with the severe organic resource limitation of deep-sea ecosystems. Our results indicate that viruses have an important role in global biogeochemical cycles, in deep-sea metabolism and the overall functioning of the largest ecosystem of our biosphere.

3

Paraphrased from abstract:

Phenotypic alterations in parasitised hosts modify host population ecology, apparent competition processes, food web structure and energy and nutrient flow between habitats, as well as favouring habitat creation.

4

Quoted verbatim from:

Researchers from the University of Connecticut discovered through modeling studies that horizontal gene transfer among microbes has the same genetic signature as common ancestry.
Horizontal gene transfer encompasses any mechanism that transfers genetic material to another organism without the recipient being the offspring of the donor.

Putting things in your own words instead of slightly restructing sentences from abstracts (or just being clear about what is quoted) generally gives people mroe confidence that you understand the subjects you’re talking about.

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By the way, this quote is a little misleading. It makes it sound as though the study analysed the sesamoid and concluded that it’s “one of the most extraordinary manipulation systems” among mammals. In other words, that the study concluded it was extraordinary in the sense that it is especially good in some way that contradicts the idea of “bad design”.

This isn’t how the quote is used at all. The quote appears in the first sentence of the abstract of this paper:
https://www.nature.com/articles/16830
The full sentence is as follows:

The way in which the giant panda, Ailuropoda melanoleuca, uses the radial sesamoid bone - its `pseudo-thumb’ - for grasping makes it one of the most extraordinary manipulation systems in mammalian evolution.

Clearly, the authors are expressing that the mere fact that the giant panda uses its sesamoid for grasping is “extraordinary” - they’re not expressing any kind of evaluation of its effectiveness. The last sentence of abstract is a more appropriate sentence to quote for that:

The radial sesamoid bone and the accessory carpal bone form a double pincer-like apparatus in the medial and lateral sides of the hand, respectively, enabling the panda to manipulate objects with great dexterity.

All this is quite irrelevant though, because to my knowledge the “bad design” argument about the Panda’s thumb has never been “the radial sesamoid provides no dexterity” - it is closer to “surely a designer would simply create a 6th finger instead of modifying a wrist bone”. I think it’s quite obvious that however dextrous the panda’s hand is with the enlarged radial sesamoid, it would be certainly more more dextrous with a 6th finger (or with a 6th and 7th finger, if you want also consider the accessory carpal).

Even if these two options were equally dextrous, the argument goes that evolution is a tinkerer that is expected to make such unusal modifications, similar to the way some orchids modify preexisting petals into traps rather than generate entirely new structures out of nowhere, as noted by Darwin.

To quote Gould:

If God had designed a beautiful machine to reflect his wisdom and power, surely he would not have used a collection of parts generally fashioned for other purposes.

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