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

[RTBsupporter]

We have decided to submit our article to a preprint server and Peer Community In (PCI) for consideration and review, following the advice of the Royal Society Open Science journal:

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Dear Dr. Rana,

I write in regard to manuscript RSOS-241574, titled “A Reboot of Owen’s Common Archetype Theory,” which you submitted to Royal Society Open Science.

Regrettably, after an initial assessment by the Editors, your manuscript has been rejected from further consideration by the journal, as they consider the paper to be beyond the scope of the journal’s Editorial Board.

While Royal Society Open Science endeavors to review and publish manuscripts from across the sciences, on rare occasions, the Editors receive manuscripts that are beyond the scope of their expertise.

In such instances, where it is unlikely that the Editors can provide rapid and comprehensive peer review, the Editors recommend that, if they have not already done so, the authors instead submit their manuscript to a field-specific preprint server and subsequently to a field-appropriate journal. [emphasis added]

In returning the manuscript to you, the Editors stress that this is not a judgment on the quality of the science, but rather a recognition that the journal cannot provide the level of service you would expect from a research journal.

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As highlighted by the journal, we have found it challenging to identify a suitable group of reviewers capable of providing the thorough and rigorous evaluation necessary to ensure that the work receives the credibility it deserves within the scientific community. While some researchers have expressed interest, many potential reviewers are either unfamiliar with the interdisciplinary nature of the content or unable to offer the detailed assessment needed to validate the article’s unconventional propositions.

I came on here to put everybody on notice about what we are doing in order to garner and help in attracting the right reviewers for our article. Once the manuscript gains approval, we can begin sharing the research with news agencies and media outlets to exponentially expand the global reach of our work.

Here is the preprint server of the article: OSF Preprints | A reboot of Richard Owen’s common archetype theory

BTW, you can call me Mac just in case people want to ask me some follow questions on this forum. Thank you.

[SkovandOfMitaze (Mi)]

Do you mean common design as in an intelligence designed life and that’s what much of it shares the same traits? If so here is an article posted here on this.

Common Descent vs. Common Design: 4 Examples Explained Better by Descent -...

[rsewell (RON SEWELL)]

@RTBsupporter

I came on here to put everybody on notice about what we are doing in order to garner and help in attracting the right reviewers for our article.

Is that not the responsibility of whatever journal ultimately accepts the manuscript?

[RTBsupporter]

They have already provided a reason why on their website:

Though it is a rare occurrence, the Editors may be unable to secure sufficient reviewer feedback to enable them to confidently render a decision on a submitted manuscript. In such circumstances, the Editor may recommend that the manuscript is returned to the author to allow them to submit their work to a suitable preprint server for community peer review, or to a more specialised journal, thus avoiding further delays on the submitted research and ensuring the research is accessible to relevant audiences as rapidly as possible.[emphasis added]
Information for authors | Royal Society Open Science (royalsocietypublishing.org)

[rsewell (RON SEWELL)]

Yes, but the message I pick up from that response is that the paper does not fit with the focus of that journal, and to seek out a more appropriate publication.

How do you see the paper? Philosophy of science, original research, survey, apologetics?

[adamjedgar (adam james edgar)]

Good luck with getting this peer reviewed favourably by anyone in the ID community (Michael Behee, Stephen Myer and the like). These guys are recognised as the goto for Intelligent Design…I cant wait to see the peer reviews as there are some significant issues between the two camps in this arena so any chance for positive appraisal will largely be left Biologos supporters (so an organisation would then be seen as self certifying which is outrageous obviously!)

I should clarify the above with a definition from the paper itself:

Definitions

Universal common designer
The cosmological constant’s remarkable precision, challenging any notion of accidental occurrence in the vast expanse of cosmological history, stands as a testament to its extraordinary nature [5,54]. Similarly, the constancy of the fine structure constant throughout the annals of the universe, as evidenced by meticulous measurements [52,107 ], and the absence of variation in the fine tuning constants further reinforces the notion of a finely crafted cosmos, where even the minutest details are meticulously calibrated [30,107]

Another issue that causes a raised eyebrow for me, given Biologos is a Christian organisation, after quickly scanning through the paper, it doesnt appear to me to be the sort of publication that is even relevant to the notion of Christianity as presented by this forum. The paper doesnt appear, as far as i can deduce presently, to utilise a shred of biblical research in any of its notions, methods, or conclusions. Surely, if a “designer” is to be considered, some biblical evidences should be also included? How does one of the Christian faith even know of a designer if one has no biblical reference from which to extrapolate the notion of “designer” within this theory?

I get the feeling this article would be at home in an atheistic environment as one could transpose common descent “designer” with the phrase “mother nature” and an atheist would have no objection to that!

[adamjedgar (adam james edgar)]

I was able to download it directly from the link in the OP.

[RTBsupporter]

@rsewell

Yes, but the message I pick up from that response is that the paper does not fit with the focus of that journal, and to seek out a more appropriate publication.

The journal does not have the usual restrictions on scope as they view it as being too subjective:

The journal covers the entire range of science and mathematics and allows the Society to publish all the high-quality work it receives without the usual restrictions on scope, length or impact. Demonstrating its commitment to best practice in open access publishing… About Royal Society Open Science | Royal Society Open Science (royalsocietypublishing.org)

Most journals base their peer review on two separate processes. The first stage is objective and assesses the rigour of the methodology and statistics, and the validity of the conclusions. The second stage is subjective and attempts to estimate the likely impact or importance of the work. Royal Society Open Science operates using the first stage only – objective peer review. As long as a submitted article fulfils the selection criteria listed above, the judgement as to its importance and impact will be left to the individual reader, the scientific community and, in the longer term, posterity. Information for reviewers | Royal Society Open Science (royalsocietypublishing.org)

@rsewell

How do you see the paper? Philosophy of science, original research, survey, apologetics?

A synthesis/conceptual review article

@adamjedgar

Surely, if a “designer” is to be considered, some biblical evidences should be also included?

It doesn’t look like you skimmed through the whole paper because it does contain the bible as evidence. Keep reading it.

[SkovandOfMitaze (Mi)]

The paper seems to be an intelligent design type of paper. It definitely won’t fit with a standard scientific journal because it’s pseudoscience. There are not atheist journals really. Just journals that demand a certain level of scientific research. I don’t know if it fits with what many here believes or not. Some believes in fine tuning and some don’t.

[glipsnort (Steve Schaffner)]

I think RTB got the editorial version of “It’s not you, it’s me”, i.e. a polite way of saying, “Don’t bother us.”

[RTBsupporter]

@glipsnort

I think RTB got the editorial version of “It’s not you, it’s me”, i.e. a polite way of saying, “Don’t bother us.”

Yes, that is definitely possible, and we have considered it. However, it seems unlikely in this case for several reasons. One is that we’ve encountered similar issues when using editing companies like Editage or Enago, which offer presubmission review services along with editing. They didn’t have reviewers in their network or on staff:

Please note, that along with being an editor, this particular expert is also a peer reviewer. As the subject area is quite niche, this is the only expert we have onboard who matches your requirement and is also available to work on your manuscript.

[Roy]

@RTBsupporter

We have decided to submit our article to a preprint server and Peer Community In (PCI) for consideration and review, following the advice of the Royal Society Open Science journal:

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Dear Dr. Rana,

…

BTW, you can call me Mac if you want to know my name and a little about me just in case people want to ask me some follow questions on this forum. Thank you.

Just highlighting that this ‘paper’ was not written by Fazale Rana and Hugh Ross of RTB, but was submitted to RSOS by some-one else masquerading as them.

This alone is grounds for rejection of both the ‘paper’ and the author.

[RTBsupporter]

@Roy

This alone is grounds for rejection of both the ‘paper’ and the author.

I don’t understand why this would be your conclusion if the paper specifically mentions in the acknowledgement section that:

I would like to thank the RTB supporters from our scholars’ community for their outstanding contributions. They provided a methodology for detecting created kinds and novel testable predictions, synthesized specific theories of quantum consciousness and process structuralism, offered potential reasons why the designer might utilize nested patterns in creation, and wrote the paper. The authors also acknowledge the assistance of ChatGPT, an AI language model developed by OpenAI, for editing this manuscript and describing how all the predictions could be tested through specific experimental designs, statistical analyses, and criteria for falsification.

I encourage you to please look further here for more information on this program: Scholar Community - Reasons to Believe

[T_aquaticus]

@RTBsupporter

Yes, that is definitely possible, and we have considered it. However, it seems unlikely in this case for several reasons. One is that we’ve encountered similar issues when using editing companies like Editage or Enago, which offer presubmission review services along with editing. They didn’t have reviewers in their network or on staff:

I highly doubt that any legitimate journal is going to publish that paper. There might be a “pay to publish” journals that would publish it, but none that have scientific merit. Having skimmed through the paper I find at least one “questionable” problem in every paragraph, and that is me being charitable.

Some general comments . . .

First, all of the quantum consciousness stuff doesn’t fit. We can watch biology happen right in front of us, including the natural processes of speciation, mutation, and natural selection producing nested hierarchies.

Second, the paper never really touches on molecular data which is where so much of the evidence supports common ancestry and evolutionary mechanisms. For example, you can find cladograms of human Y chromosome data that was produced by evolutionary mechanisms.

Third, you are running headlong into parsimony. The paper has the thinnest of arguments for why a designer would choose a nested hierarchy, and even ignores the fact that human designs regularly do not fall into a nested hierarchy. On top of this, the mechanisms offered are not observed as they are with the natural process of evolution. You are asking scientists to accept that design would produce a nested hierarcyhy for no good reason, and then reject known and observed natural processes that are known to produce a nested hierarchy. Parsimony goes with the observed process.

[RTBsupporter]

@T_aquaticus

I highly doubt that any legitimate journal is going to publish that paper. There might be a “pay to publish” journals that would publish it, but none that have scientific merit.

The issue raised by the journals we’ve submitted to hasn’t been the scientific merit of the work itself. Instead, it’s largely been due to the paper being highly specialized and unconventional, which makes it difficult for their reviewers and editors to assess. The RSOS journal is a perfect example of this as I pointed out in the OP and in subsequent responses.

@T_aquaticus

Having skimmed through the paper I find at least one “questionable” problem in every paragraph, and that is me being charitable.

We appreciate all critical feedback, and there is no need for charity in your assessment. We value constructive and detailed critiques that help sharpen the arguments presented.

@T_aquaticus

First, all of the quantum consciousness stuff doesn’t fit. We can watch biology happen right in front of us, including the natural processes of speciation, mutation, and natural selection producing nested hierarchies.

This seems to highlight the challenge we’ve faced in finding the appropriate reviewers for the paper in a timely fashion. Evaluating the integration of quantum mechanics, particularly quantum consciousness, requires a background in both quantum physics and biology. Without that interdisciplinary expertise, it’s difficult to assess the relevance of the quantum aspect to our overarching model.

@T_aquaticus

Second, the paper never really touches on molecular data which is where so much of the evidence supports common ancestry and evolutionary mechanisms. For example, you can find cladograms of human Y chromosome data that was produced by evolutionary mechanisms.

We don’t overlook molecular data; rather, we incorporate it within the framework of Owen’s extended theory to offer an alternative explanation. In the section “Common Design from a Common Designer,” we engage with molecular data and emphasize that human designs often do not follow strict nested hierarchies due to intentional design constraints, and this analogy applies to our approach in nature.

@T_aquaticus

The paper has the thinnest of arguments for why a designer would choose a nested hierarchy…

It’s unclear what specific arguments you are referring to here. We provide a detailed rationale in the section “Reasons for Choosing Nested Patterns,” where we explain why nested hierarchies might be a natural outcome of design principles when viewed through the lens of Owen’s theory

@T_aquaticus

On top of this, the mechanisms offered are not observed as they are with the natural process of evolution.

In the section “Reasons for Choosing Nested Patterns,” we do outline observable mechanisms that support our model. We provide specific ways to test these mechanisms, which are grounded in Owen’s theory, and argue that they offer a plausible explanation alongside natural processes.

@T_aquaticus

You are asking scientists to accept that design would produce a nested hierarcyhy for no good reason, and then reject known and observed natural processes that are known to produce a nested hierarchy. Parsimony goes with the observed process.

We are not asking scientists to reject known natural processes. Rather, we are proposing that Owen’s alternative explanation for the nested hierarchy, based on design principles, is worth reconsidering and testing. Our model is not incompatible with natural processes but instead seeks to extend current explanations with additional layers of design-oriented interpretation, which we argue can be empirically tested.

[T_aquaticus]

@RTBsupporter

The issue raised by the journals we’ve submitted to hasn’t been the scientific merit of the work itself. Instead, it’s largely been due to the paper being highly specialized and unconventional, which makes it difficult for their reviewers and editors to assess.

That’s them being nice.

@RTBsupporter

Evaluating the integration of quantum mechanics, particularly quantum consciousness, requires a background in both quantum physics and biology. Without that interdisciplinary expertise, it’s difficult to assess the relevance of the quantum aspect to our overarching model.

What is the relevance at the level of biology and heritable traits? How is it relevant to which mutations occur, or which traits are passed on? How are its effects seen in the molecular data?

@RTBsupporter

We don’t overlook molecular data; rather, we incorporate it within the framework of Owen’s extended theory to offer an alternative explanation.

Molecular data is only mentioned in generalities. You will need to dig into the specifics in at least one area. For example:

They embody fundamental structural blueprints or archetypes, allowing interaction with host cells through convergent co-option. This process, observed in the shared ERV gene repurposed across distinct mammalian orders, exemplifies convergent co-option [82]. Furthermore, non-random mutations and HGT could be interpreted as mechanisms driven by this adaptive force, enabling viruses to adapt to environmental pressures. Similar to Owen’s theory, viruses evolve through a combination of inherent structural characteristics (polarizing force) and adaptive modifications (adaptive force).

First, what is “convergent co-option” and what does it look like at the sequence level? Also, why isn’t the observed process of viral integration a better explanation for the presence of these insertions? How many of the 200,000 human ERV’s even show signs of function? Where is the sequence level evidence of non-random mutations? How can polarizing force and adaptive force be measured in sequence data? Examples for any of these?

@RTBsupporter

It’s unclear what specific arguments you are referring to here. We provide a detailed rationale in the section “Reasons for Choosing Nested Patterns,” where we explain why nested hierarchies might be a natural outcome of design principles when viewed through the lens of Owen’s theory

It makes no sense:

The law of entropy exemplifies this polarizing and adaptive force in action, as it explains how evolution emerges with functional, self-organizational order through energy dispersal by gradient reduction, serving as the motive force behind hierarchical organization [1]. This universal law transcends the boundary between animate and inanimate systems, as both evolve through energy flows toward stationary states relative to their surroundings [1].
. . .
In software engineering, principles like easier maintenance, code reuse, and scalability are closely tied to the concept of nested hierarchy [31]. While strict adherence to hierarchies may not always be suitable, engineers have recognized their utility in designing complex systems more efficiently [33]. Similarly, analogous principles and nested hierarchies are observed in biological systems, where concepts like survivability, reproduction, and adaptations mirror software engineering principles

First off, the programs I write do not fall into a nested hierarchy. I use different modules in different combinations all of the time. There is absolutely no reason why different programs should fall into a nested hierarchy.

The rest of it makes no sense. Why would entropy be responsible for producing a nested hierarchy? Also, human designed organisms that violate a nested hierarchy (i.e. genetically modified organisms) survive just fine.

@RTBsupporter

In the section “Reasons for Choosing Nested Patterns,” we do outline observable mechanisms that support our model. We provide specific ways to test these mechanisms, which are grounded in Owen’s theory, and argue that they offer a plausible explanation alongside natural processes.

Like what?

[rsewell (RON SEWELL)]

@RTBsupporter

We appreciate all critical feedback, and there is no need for charity in your assessment.

Given that…

In software engineering, principles like easier maintenance, code reuse, and scalability are closely tied to the concept of nested hierarchy

I echo @T_aquaticus here; almost every substantial working piece of software out there violates nested hierarchy. Easier maintenance, code reuse, and scalability, are mostly tied to scoping of parameters and functions so that modules have the independence to be plugged in without conflict. You can then remove, say, a dialog box and replace with a preferable module, perhaps even written in another language. Being able to import, mix, and match without regard to hierarchy or dependency is the objective. That is the very opposite of a tree structure.

[RTBsupporter]

@T_aquaticus

@RTBsupporter

The issue raised by the journals we’ve submitted to hasn’t been the scientific merit of the work itself. Instead, it’s largely been due to the paper being highly specialized and unconventional, which makes it difficult for their reviewers and editors to assess.

That’s them being nice.

Like I said before, that’s definitely a possibility, and we’ve considered it. However, there are reasons to think otherwise beyond what I’ve already mentioned. One important factor is the time it took them to decide—over two weeks. If they were just being polite and dismissing the paper, they would have likely made a faster decision to avoid wasting either their time or the author’s time.

@T_aquaticus

What is the relevance at the level of biology and heritable traits?

Owen’s enhanced theory suggests that microtubules might be sites of quantum coherence. If this is true, quantum effects could influence biological processes like gene regulation, mutation outcomes, and heritable traits. This includes processes that govern how traits are passed on to future generations.

@T_aquaticus

How is it relevant to which mutations occur, or which traits are passed on?

According to the theory, the collapse of the quantum wave function within microtubules might occur at critical moments in cellular processes, possibly influencing mutation events. This would mean that certain quantum possibilities within the genetic code could collapse into specific outcomes, potentially affecting which mutations arise and, by extension, which traits are passed on.

@T_aquaticus

How are its effects seen in the molecular data?

If quantum consciousness has a significant role in biological processes, we would expect to see non-random patterns in molecular data, such as increased efficiency and speed in processes like gene expression or mutations. Such patterns could indicate quantum-induced variability, which would not be fully explained by classical genetic models.

@T_aquaticus

Molecular data is only mentioned in generalities. You will need to dig into the specifics in at least one area.

The studies we referenced offer the detailed mechanisms you’re asking for. These include discussions of specific cases where quantum processes might influence biological outcomes.

@T_aquaticus

First, what is “convergent co-option” and what does it look like at the sequence level?

For a more detailed answer, you can refer to this study:
J. Simpson, C.A. Kozak, G. Boso, Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLOS Genet. 18, e1010458 (2022), PMID: 36240227, PMCID: PMC9604959.

@T_aquaticus

Also, why isn’t the observed process of viral integration a better explanation for the presence of these insertions?

Not quite sure what you are getting at here, but it’s not that we are suggesting viral integration is a lesser explanation; rather, we are proposing that there may be additional mechanisms involved beyond the conventional ones, which could further explain the phenomenon.

@T_aquaticus

How many of the 200,000 human ERV’s even show signs of function?

Our theory predicts that over 80% of these ERVs show signs of function, particularly in roles related to gene regulation and immune responses.

@T_aquaticus

Where is the sequence level evidence of non-random mutations?

We mentioned this in the subsection “Universal Common Designer”.

@T_aquaticus

How can polarizing force and adaptive force be measured in sequence data? Examples for any of these?

We mentioned this section "More falsifiable predictions and methods of testing "

@T_aquaticus

First off, the programs I write do not fall into a nested hierarchy. I use different modules in different combinations all of the time. There is absolutely no reason why different programs should fall into a nested hierarchy.

That’s true, and it depends on the design objectives. In software, modular design often avoids hierarchical structures for flexibility, but in biology, the analogy might be different. We propose that in biology, nested hierarchies could arise due to the efficiency and speed of evolutionary design principles, which often lead to tree-like structures as we observe in phylogenetic data.

@T_aquaticus

Why would entropy be responsible for producing a nested hierarchy?

This study should give you the answer:
A. Annila, E. Kuismanen, Natural hierarchy emerges from energy dispersal. Biosystems 95, 227–233 (2009). [Epub 2008 November 6]. PMID: 19038306.

@T_aquaticus

Also, human designed organisms that violate a nested hierarchy (i.e. genetically modified organisms) survive just fine.

@rsewell

I echo @T_aquaticus here; almost every substantial working piece of software out there violates nested hierarchy. Easier maintenance, code reuse, and scalability, are mostly tied to scoping of parameters and functions so that modules have the independence to be plugged in without conflict. You can then remove, say, a dialog box and replace with a preferable module, perhaps even written in another language. Being able to import, mix, and match without regard to hierarchy or dependency is the objective. That is the very opposite of a tree structure.

Since using nested patterns is recognized by engineers to be more efficient and faster in designing complex systems, we infer that these reasons can be applied to biology as well, especially when analogous principles and nested hierarchies are observed in biological systems. However, we don’t know whether this is true or not yet, but we do describe ways to test it in section “Falsifiable predictions”.

[rsewell (RON SEWELL)]

@RTBsupporter

Since using nested patterns is recognized by engineers to be more efficient and faster in designing complex systems, we infer that these reasons can be applied to biology as well, especially when analogous principles and nested hierarchies are observed in biological systems.

No, you cannot infer this, because the principles are not analogous. Scoping is entirely different from a nested hierarchy. Millions of people code and are pretty aware of what they do and do not recognize, so good luck convincing many with your line of argument.

The biological nested hierarchy rests on a simple and accessible fact that does not apply to software, Ford F-150s, or any real deployed technology. Offspring look a lot like their parents, and that is due to the constraints of reproduction.

[T_aquaticus]

@RTBsupporter

Like I said before, that’s definitely a possibility, and we’ve considered it. However, there are reasons to think otherwise beyond what I’ve already mentioned. One important factor is the time it took them to decide—over two weeks. If they were just being polite and dismissing the paper, they would have likely made a faster decision to avoid wasting either their time or the author’s time.

In my experience, two weeks is pretty fast.

@RTBsupporter

Owen’s enhanced theory suggests that microtubules might be sites of quantum coherence. If this is true, quantum effects could influence biological processes like gene regulation, mutation outcomes, and heritable traits. This includes processes that govern how traits are passed on to future generations.

How?

@RTBsupporter

If quantum consciousness has a significant role in biological processes, we would expect to see non-random patterns in molecular data, such as increased efficiency and speed in processes like gene expression or mutations. Such patterns could indicate quantum-induced variability, which would not be fully explained by classical genetic models.

By molecular data, I mean sequence data as in the DNA sequence differences between organisms.

@RTBsupporter

The studies we referenced offer the detailed mechanisms you’re asking for. These include discussions of specific cases where quantum processes might influence biological outcomes.

They need to be biological processes that affect heritable traits at the DNA level. This again means differences in DNA sequences.

@RTBsupporter

For a more detailed answer, you can refer to this study:
J. Simpson, C.A. Kozak, G. Boso, Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders. PLOS Genet. 18, e1010458 (2022), PMID: 36240227, PMCID: PMC9604959.

How does this indicate design?

@RTBsupporter

Not quite sure what you are getting at here, but it’s not that we are suggesting viral integration is a lesser explanation; rather, we are proposing that there may be additional mechanisms involved beyond the conventional ones, which could further explain the phenomenon.

Based on what evidence?

@RTBsupporter

Our theory predicts that over 80% of these ERVs show signs of function, particularly in roles related to gene regulation and immune responses.

Based on what evidence?

@RTBsupporter

We mentioned this in the subsection “Universal Common Designer”.

So what is it? What is the evidence for non-random mutations?

@RTBsupporter

We mentioned this section "More falsifiable predictions and methods of testing "

And they are?

@RTBsupporter

We propose that in biology, nested hierarchies could arise due to the efficiency and speed of evolutionary design principles, which often lead to tree-like structures as we observe in phylogenetic data.

What is meant by " efficiency and speed of evolutionary design principles"?

@RTBsupporter

This study should give you the answer:
A. Annila, E. Kuismanen, Natural hierarchy emerges from energy dispersal. Biosystems 95, 227–233 (2009). [Epub 2008 November 6]. PMID: 19038306.

I don’t see how. Could you explain how these concepts apply to nested hierarchies in biology?

@RTBsupporter

Since using nested patterns is recognized by engineers to be more efficient and faster in designing complex systems,

Do they? Do engineers force all of their different designs into a nested hierarchy? From what I have seen, it is just the opposite. Human genetic engineers regularly violate a nested hierarchy when they design organisms. My python and R scripts violate a nested hierarchy all of the time.

Think about it. Would a car engineer not add a turbo to an engine because it might violate a nested hierarchy?