Can a Common Design model be useful?


Previously, I argued that the God hypothesis can be scientifically useful. Please read post 326 in this source to get the lastest revised summary of my hypothesis: Can God be a useful “scientific” hypothesis? Yes - Peaceful Science

This topic will be an add on to what I argued there. I aim to show that the Universal Common Design model can be useful, but this time the designer in question will be the Judeo-Christian God.

However, it is important to note that this theory will still not offer an explanation for how consciousness arose. This means that the model will not attempt to explain how the universe was created and developed.


There are two confirmed predictions that really support the idea that the Garden of Eden existed and the interactions between God and man that led to the fall of humanity actually took place.

For instance, Genesis 2 claims that the Pishon, Gihon, Tigris, and Euphrates Rivers all meet together in Eden. Instead, as skeptics have pointed out, nowhere on the planet do the four rivers come together as Genesis 2 suggests.

However, all four rivers do flow into different parts of the Persian Gulf. And it now appears the four rivers would have converged in what a researcher, named Rose, identifies as the Gulf Oasis. According to his study, the Persian Gulf region was once a lush oasis, during the last glacial maximum. The study described four rivers, the Tigris and Euphrates Rivers from Mesopotamia, the Karun River (biblical Pishon?) draining the Iranian Plateau, and the Wadi Batin River (biblical Gihon?) flowing across northern Arabia.

New Light on Human Prehistory in the Arabo-Persian Gulf Oasis | Current Anthropology: Vol 51, No 6 (

Lost Civilization May Have Existed Beneath the Persian Gulf | Live Science

As Rose points out, the Gulf Oasis was also watered by springs upwelling from subterranean aquifers. Genesis 2:6 also states that “streams came up from the earth and watered the whole surface of the ground.” Genesis 7:11 identifies “springs of the great deep” as part of the source of the flood waters that wreaked havoc upon the ungodly of Noah’s generation, which would explain why today’s geography is different compared to the past. Thus, the Gulf Oasis vindicates the unique claims Genesis makes about the Garden of Eden and its surroundings.

So the question now becomes…

What if all living organisms have a common design from a universal common designer?

Universal Common Design Theory

A Universal common designer re-uses a DNA blueprint, microbial organisms, and chemical constituents to separately construct plants, birds, insects, herbivore mammals, carnivorous mammals, sea mammals, and different locations around the globe.

There are three key differences between common design and common descent predictions…

Common Design:

A) Most vestigial features have a function
B) These functional features are fully optimal under different environments.
C) Examples of Convergent evolution are ubiquitous

Common Descent:

A) Vestigial features have no function
B) Functional features are suboptimal under a particular environment
C) Examples of Convergent evolution are rare


If this is true, we should find functional Endogenous retroviruses and Pseudogenes between species

If this is true, we should find more examples of horizontal gene transfer among Eukaryotes

If this is true, we should find many more examples of domestication from bird and mammal species

If this is false, we would find examples of animal behavior displaying forms of digital information according to RTB, such as…

  1. Capacity for symbolic expression
  2. Ability to invent and manipulate symbols
  3. Ability to invent and manufacture complex tools
  4. Capacity for explosive technological advance
  5. Ability to manufacture and wear clothes
  6. Ability to invent and use complex languages
  7. Capacity to form complex social structures
  8. Ability to invent and use complex trading and transportation systems
  9. Ability to engage in mathematics, literature, philosophy, and theology
  10. Ability to tame, domesticate, and train nephesh animals

This is one big unsubstantiated pile of claims and some are contradicted by massive swaths of data. All the data points to the shared ancestry of plants, animals, insects and microbes, not a separate emergence for each.

None of these are predictions of common descent.

A) Most vestigial structures in organisms which share a common ancestor can acquire new functions as well. This does not separate common ancestry from design.

B) I have lungs which are optimized for gaseous exchange on land. In water though, they are completely useless for breathing. Your common design hypothesis is falsified.

C) Provide evidence that convergent evolution is ubiquitous.

First, why would you want to find a functional endogenous retrovirus in your genome? That’s insane! I take it you mean we expect to find functional ERV elements or pseudogenes and we indeed have uncovered some. In any case, common descent is silent on whether an inherited feature (pseudogene or ERV element) is functional or not. In addition, why do pseudogenes exist at all since their functional versions must have been “fully optimal under different environments”?

Second, common descent is also silent on the extent of horizontal gene transfer, whether its between two eukaryotes, prokaryotes or eukaryote-prokaryote pair.

Third, common descent has nothing to do with animal domestication. I wonder where you pick these nonsense ideas from.

  1. Animals that manufacture and wear clothes? Humans of course. That wasn’t hard to find. We also do every other thing on your list. I guess humans have falsified your hypothesis.

  2. Some other animals seem to have evolved the ability to use complex language:

  1. Some other animals have complex social structures:

Sorry, but the rivers don’t flow into Eden; they flow out of Eden. And the Gihon is usually identified with the Nile, as Kush is usually identified with Egypt. I’m not seeing what any of this has to do with a common design model.

What translation are you using? Most translations say “a mist”, not “streams”. Further, Noah’s flood subsided, while the flood of the Persian Gulf oasis (a very gradual one, taking centuries) never did. Nor is the place of the flood, or where Noah lived, identified as being anywhere near Eden.

It vindicates none of them.

These are not predictions of common descent, so you are providing a strawman model here.

Please explain this model is better detail. What exactly was separately constructed? Each species? Each family? Each phylum? What? Now, the greatest failing of common design is that it has no expectations and explains nothing. It certainly fails to explain the nested hierarchy in which species are arranged.

Why? That’s not a prediction of common design.


Many more than what? And why?

Why? How are any of those “digital information”?

I’m afraid that none of that made any sense. Your predictions are not predictions of common design, or common descent, and you have ignored the major predictions of common descent that distinguish it from common design. This is more word salad.


Hi Meerkat
Here is an alternative creation model from Winston Ewert if you have not seen it.

A writer in the Middle East 2500 hundred years ago could have easily written a story about a garden where four rivers meet. It is still fiction. It says nothing about the existence or non-existence of God.


Likewise a universal common design also says nothing about the existence or non-existence of God. Universal common design does not say God did it or God didn’t do it as a science is neutral on whether God exists or not.


It’s not actually a creation model. It’s not a model of anything. It’s just a graph with gene distributions plotted on it, and the groups are ad hoc: just whatever set of genes has that distribution. Does Ewert attempt an explanation of what that graph represents? What do you think it represents?

1 Like

Focus more on whether the model is potentially useful rather than true.

Convergent Evolution: Limited Forms Most Beautiful (Vienna Series in Theoretical Biology): Jr., George R McGhee: 9780262016421: Books

Life’s Solution: Inevitable Humans in a Lonely Universe: Conway Morris, Simon: 8601420433298: Books

Fuz Rana, from RTB:

"The research team from Germany, the US, and Australia detected variants of the endogenized KoRV in koala genomes that appear to be a combination of KoRV and other preexisting ERVs also found in the koala genome. In other words, it appears as if preexisting ERVs in the koala genome—through the process of retrotransposition—inserted copies of themselves into endogenized KoRV, disrupting their sequence and, consequently, disabling them. The researchers concluded that this process doesn’t appear to require the DNA sequence of the preexisting ERV to bear any similarity to the KoRV.

In other words, the research team discovered that preexisting ERVs play a role in imparting koalas with an innate immunity against KoRVs. In fact, the researchers believe that this mechanism may be widespread among animals, including humans. If so, the ERVs embedded within genomes serve as an antiviral defense system."

Degradation and remobilization of endogenous retroviruses by recombination during the earliest stages of a germ-line invasion | PNAS

Fuz Rana:

"If the creation model perspective on ERVs is valid, then it suggests that ERVs may protect the host cell’s genome from retroviral infections through other mechanisms, like competitive inhibition. Most ERV sequences, like retroviral genomes, consist of two noncoding regions on the 3´ and 5´ ends of the sequence called long terminal repeats (LTRs). The ERV sequences also contain genes for reverse transcriptase and the proteins located in the virus capsule. If the ERV sequence is transcribed to produce ERV RNA and if the capsid proteins are produced, then both the RNA and the capsid proteins could inhibit the assembly of invading retroviral particles, through competitive inhibition, which would prevent the transmission of the invading retrovirus to other cells. In this scenario, the similarity of the ERVs to retroviruses is crucial.

This proposed antiviral mechanism has been observed by researchers from Imperial College London in the UK. They detected a conserved ERV sequence in the genomes of humans, sheep, mice, and rats. They found this sequence to be under the influence of purifying selection. In other words, the sequence must be functional. It codes for proteins that are similar to those found in retroviruses. The researchers speculate that when these genes are transcribed and translated, they interfere with the assembly of retroviruses.

The bottom line: ERVs serve at least one function, accounting for their presence in genomes from a creation model vantage point. In light of this function, a rationale indeed exists for their structural and functional similarity to retroviruses."

A Co-opted gypsy-type LTR-Retrotransposon Is Conserved in the Genomes of Humans, Sheep, Mice, and Rats - ScienceDirect

Indirectly speaking, it does actually. It confirms a prediction from the Adam and Eve story as well as Noah’s story, in which I derived my common design model from. As you know, common descent suggests we came from another animal.

Were you trying to be funny here? Under the common design model, we are not animals but created separately and uniquely.

Humans influencing domesticated animals to mimick their behavior does not count as evidence that they created NEW digital information.

As you know, common descent suggests we came from another animal.
I derived my common design model from the Adam and Eve story as well as Noah’s story to potentially show that it is the Christian God and confirm those stories.

In the study I gave you already, Rose points out that during the late Pleistocene era (150,000 to 12,000 years ago) reduced sea levels periodically exposed what’s called the “Gulf Oasis.” The Persian Gulf receded far enough to expose a landmass as large as, or larger than, Great Britain. Rose reports this landmass was well-watered by four rivers fed at the time by snow and ice melt: the Tigris, Euphrates, Karun, and Wadi Al-Bāṭin. More than 60 archeological sites, some of which are currently submerged, show that the area was extensively inhabited.

Biblical place names and other descriptive details in the first two chapters of Genesis, including the mention of four major rivers, point to this locale as the likely vicinity not only of Eden but also of the world in Noah’s time. Based on humanity’s refusal to disperse even after the flood we can surmise this is where many of Noah’s descendants continued to dwell.

The archaeological remains of ancient human settlements there would, of course, belong to postflood people, given that any traces of preflood habitation would have been destroyed in the inundation. From a geographical perspective, this location makes sense as the region where the flood occurred. It was habitable and arable roughly 50- 40,000 years ago, a rough estimate of when Noah lived. More importantly, during this time and location, a population bottleneck occurred where the number of humans plummeted, and the shrinking remnant became more genetically similar.

Huge aquifers reside under this region, the potential “springs of the deep” mentioned in the account, and high mountains surround it. In addition, it offers a fairly easy migration route into eastern Africa, where genetic diversity is high. Taking all these factors (and more) into account, the latest scholarship proposes that the Genesis flood covered all of Mesopotamia, the entire Persian Gulf region, and much of southern Arabia, as well.

From RTB, Navigating Genesis.

Apparently, many biologists would disagree with you as I showed Michael on here.

From AJ Roberts at RTB:

"…created kinds cannot be defined a priori but must be determined through observations and comparisons. And due to the somewhat arbitrary nature of various taxa, “kinds” may not be definable across taxa. For example, some created “kinds” might fall at the level of phyla and others at the level of class. Perhaps other “kinds” would even fall at the level of species or subspecies (e.g., Homo sapiens sapiens ).

“…as far as nested hierarchies go, there’s a bit of a challenge because a progressive creation model would also expect nested hierarchies within clades or created kinds. However, a progressive creation model would also predict that there are independent hierarchies (unrelated organisms), each stemming from an organism created by fiat and filled out through secondary cause-and-effect reproduction. These original created organisms would not be static but dynamic, able to adapt to changing environments and diversify over long epochs of time and would entail many familiar mechanisms such as epigenetic changes and gene flow.”

“…Is there a prediction that stems from a progressive creation model’s assertion of independent hierarchies (even if containing nested hierarchies within)? One might imagine that as scientists continue to sequence more and more environmental samples or newly discovered organisms, some organisms will emerge that do not fit nested hierarchies already in place. Newly discovered (and sequenced) organisms should fit into the ever-bushier plethora of nested hierarchies depicting evolution’s common descent from the last universal common ancestor in the evolutionary model. In contrast, if true, progressive creationism would predict that independent hierarchies may be discovered.”

Yes, it is. For more, read my reply to @Michael_Okoko unless you want me to repeat everything.

Can you tell me what those predictions would be that distinguish it from common design? I want to know your thoughts on it.

The geography at that time was drastically different. This means the human writers would not have been able to use human reason and experience to suggest the Pishon, Gihon, Tigris, and Euphrates Rivers all meet together in Eden; Otherwise, skeptics would not have pointed out that nowhere on the planet do the four rivers come together as Genesis 2 suggests.

Please read my introduction again.

Just want to point out that there’s nothing about common ancestry that implies convergence should be rare.


Okay and point out that there’s a boatload of “suboptimal” features all over the place.


And note that some actually very specific testable predictions from “common design” are false. For example, non-functional sequences, like degraded ERV insertions, should not follow the same nested hierarchical pattern found in “functional” sequences. (Because they appear and mutate in a non-deterministic way, so independently “designed” lineages should be uncorrelated.) And yet…


Your hypothesis is not useful because it can explain everything. God could have created all life forms via common descent, direct creation or both. Since you can’t read God’s mind, its impossible to tell which strategy he adopted making your hypothesis untestable at its core and practically useless.

I asked for evidence not books, where is it? More importantly have you read these books? If yes, you could highlight parts of the books that demonstrate ubiquity of convergent evolution.

This quote from Fuz Rana is completely irrelevant. It makes no mention of common descent or how it predicts the existence of functional ERV elements. More so, I previously agreed some ERV elements can pick up new functions as time progressed.

You seemed not to understand why I questioned your desire to find functional ERVs in our genome. Every cell in your body has a genome with ERVs and ERV elements. If these ERVs were functional (that is, if they could be expressed) every cell in your body would be flooded with infectious, replication-competent virus particles. You would literally dissolve alive. That’s why you should be talking about functional ERV elements like co-opted LTRs, not full-length transcriptable ERVs.

Another irrelevant quote from Fuz Rana, this time on three counts as there is no mention of common descent, eukaryotic horizontal gene transfer or a link between both. This shows, like before, that you are clueless about the issues you raise here. You just quote your creationist heroes whether their statements are relevant or not to a discussion.

And it seems Fuz Rana is under the impression that since some functional ERV sequence elements have been found, therefore all other ERV elements are functional. That makes two wrong people on this thread.

You are not making any sense. Animal domestication has nothing to say about common descent. Another big pile of gibberish from you.

Humans eat, sleep, produce offspring, poop, communicate with others, mate, are carbon-based, die, etcetera like every other animal you and I know. Yes, on average we are smarter than other animals, but some other animals are faster, physically stronger and have even displayed intelligent feats comparable to that of humans. Regardless, humans are classified as animals in biology because we possess traits that all other animals have as well. That’s basic biology which you just demonstrated ignorance of.

We are a unique species no doubt, but in a given context. Other animals are unique in other contexts. IMO the most outstanding organisms are microbes: without them we would not survive, but they have been around for billions of years and contributed to making this planet habitable for you and I.

Prairie dogs are not domesticated, neither did the researchers mimic their behavior. Its just clueless you blabbing again. Whatever the case, you claimed we shouldn’t find complex language systems or societal structures in the wild, but we found some, so that leads us to reject your hypothesis.

Your latest remarks indicate you are not here to learn, but do apologetics. This makes it pointless engaging further with you, so I gladly retire myself from this discussion. Gracias.



The hierarchical classification of life has been claimed as compelling evidence for universal common ancestry. However, research has uncovered much data which is not congruent with the hierarchical pattern. Nevertheless, biological data resembles a nested hierarchy sufficiently well to require an explanation. While many defenders of intelligent design dispute common descent, no alternative account of the approximate nested hierarchy pattern has been widely adopted. We present the dependency graph hypothesis as an alternative explanation, based on the technique used by software developers to reuse code among different software projects. This hypothesis postulates that different biological species share modules related by a dependency graph. We evaluate several predictions made by this model about both biological and synthetic data, finding them to be fulfilled.

The abstract seems pretty clear. The pattern is similar to a module sharing which is a technique of software design.

So it’s completely ad-hoc, and fundamentally untestable.


What specific, testable predictions can be made based on this dependency graph idea that allow one to distinguish that explanation from common ancestry?

1 Like

But those aren’t modules in any meaningful way. They’re just arbitrary assemblages of genes that happen to have the same distribution, given the current taxon sample. That’s not a model, and it describes no process. What, in reality, does this dependency graph represent?

Nor can this “dependency graph” model be extended past the simple presence or absence of genes and into other sorts of phylogenetic data.

1 Like

Nothing you said was any sort of substantive reply to anything I said. For the most part you either ignored it outright or just repeated what you had said previously. If you really want anyone to engage with your question you’re going to have to do better than that. I suggest starting over with my reply, consider each and every point, think about how it impacts your “model”, and respond fully and reasonably.

I already told you, and the evidence that you want to know my thoughts is sparse, considering that you have ignored most of them. The major prediction of common descent is nested hierarchy. On this we agree, apparently, since you accept that nested hierarchy occurs within kinds but not between them. That means that any species that are part of a nested hierarchy are the same kind as other species in the hierarchy, right? But Homo sapiens is part of the same nested hieararchy as other primates, other mammals, other tetrapods, other animals, other eukaryotes, at least. Past eukaryotes it gets a little muddier, given the extensive fusion and horizontal transfer. But there seems at least a nested hierarchy of archaea, with core parts of the eukaryote genome nested within it.

Thus, at minimum, by your own reasoning (well, your borrowing from RTB), Eukaryota is a single kind. That much seems clear enough. And yet you reject that conclusion. A common design model is in fact not useful; it’s the opposite of useful.

One more point: you, like most creationists, confuse the difference between common descent vs. separate creation with the difference between natural and guided evolution. These are two entirely separate questions, and most of your “predictions”, if they’re anything at all, deal with the second one, not the first. Thus if convergence, for example, is greater than expected under the natural evolution model, it might be explained by God’s forcing of convergence during evolution. (And of course the fossil record frequently confirms this in such cases, common descent from more dissimilar forms to superficially similar ones.)

So, start over. Deal with my first reply. Then deal with this one. Actually read them, understand them, think about them, and make real replies.


Not at all.

If a new video card, or next generation wi-fi standard is released, the API can be addressed in C, Visual Basic, Python, or any number of contemporary, independently branched languages.

Other than a limited role for HTG [horizontal gene transfer], nature cannot do this. Once forks in the hierarchy have been passed, modifications in one branch are not assessible for distribution to the tips of other branches. Software objects can do exactly this because they actually are intelligently designed. That is the entire idea of plug ins.

What we observe is that while a Creator should be able to share modules similarly to software design, nature in fact displays constraint, so that only features which are accountable by common descent are found. If God created the hierarchy, He did so in a way which was in practice and principle indistinguishable from common descent, and thus beyond falsification.


Hi Dave
Its been awhile since I looked at it but what I remember is that it explains a pattern of common and de novo modules (gene patterns). We would also not expect that pattern to follow the tree all the time. This is similar to the software design method of reusable modules.

For ID to have a cohesive theory then the patterns would follow Mike Behe’s design detection method of observing a purposeful arrangement of parts. In the case of this hypothesis the parts would be genes. The graphs that Winston uses are pretty complex but his concept is explained in a simpler graph or Venn diagram I call “Sals flower” as @stcordova (Sal) first introduced it at TSZ

What would be interesting is to begin to find how and if these unique gene sets build these distinctly different animals.

Nor does evolutionary theory.

“Purposeful arrangement of parts” is not testable. It’s squishy.

What I mean is, earlier in the thread, I provided competing predictions from common descent and common design regarding the distribution of ERV insertions. The actual distribution matches the evolutionary prediction, and contradicts the design prediction.

What is another such prediction, specifically based on this dependency graph concept, that one can use to evaluate the competing explanations?


No, it doesn’t explain them. It just shows them. And a module is nothing like a gene pattern. The former is, presumably, functionally linked, while the latter exists even if genes arise and are lost at random. These “modules” are completely ad hoc and without explanation. On the other hand, gene gain and loss during evolution on a particular tree is an explanation of the pattern.

1 Like

The main conclusion/prediction of the paper is that the dependency graph is a better fit for the data (dependent gene sets) than a tree.
Page 10 of the paper describes the results.