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

[RTBsupporter]

@glipsnort

Look, you said you were looking for peer review. That’s what I’m giving you. My background is in both particle physics and biology, including evolutionary biology, and I’ve published extensively in both fields. I’ve also annoyed some researchers by being willing to take creationists seriously.

If you’re genuinely trying to offer peer review, then why give up on the discussion already? Shouldn’t you allow me the opportunity to respond to what you’ve said?

@glipsnort

Sorry, but you simply did not provide a mechanism by which dark energy or microtubules would generate the necessary wave function collapse: one that causes specific macro events like horizontal gene transfer, rather than, say, causing all living horses to simultaneously turn into polka-dotted rutabagas – also macro events that are highly unlikely under quantum mechanics. There is no theory underlying which events occur via this mechanism.

You’re conflating our theory with Penrose’s Objective Reduction (Orch-OR) theory. In our model, the wave function collapses spontaneously without external forces, making it a more parsimonious theory than Orch-OR or String Theory. I encourage you to read the section on “Human Consciousness” for a better understanding of the differences between these theories.

@glipsnort

What you do provide is a vague analogy between the universal wave function (which you assert incorrectly is an empirical reality) and Owens’s notion of platonic archetypes, even though they’re conceptually very different.

We never stated that the wave function is an empirical reality. Rather, we argue that empirical evidence supports the existence of the universal wave function. There’s a subtle but important distinction here. Regarding Owen’s archetype, it’s worth noting that he didn’t provide a rigorous, concrete description, and even acknowledged not fully understanding its nature. His archetype was abstract, rooted in Platonic philosophy. Owen’s model, influenced by biblical concepts, may have drawn from the Bible’s description of the “Word” as a reasoning or divine expression. Similarly, Penrose’s Platonism informs his view of the universal wave function. Given both Owen’s and Penrose’s reliance on Platonic ideals, it’s not clear why you would argue they are conceptually very different.

@glipsnort

You then treat the two as equivalent and as the same as a universal designer, all without any real support.

That’s not accurate. We specifically cited a review article in the same section that supports our analogy.

@glipsnort

Peer review only works if you are willing to listen to what the reviewers are telling you. And what I’m telling you is that this is not a scientific paper.

I understand that our paper may not conform to traditional scientific formats, which can lead some to perceive it as non-scientific. However, the ideas are rooted in rigorous reasoning and deserve careful consideration.

@Roy

You earlier wrote that you did predict that specific 80% number. So you cannot be trusted.

At the time, I was specifically referring to endogenous retroviruses (ERVs), where the 80% functionality prediction remains unconfirmed. In contrast, the ENCODE project confirmed that 80% of junk DNA overall has functional activity. To clarify, our hypothesis about 80% of ERVs being functional arises from a synthesis of Owen’s archetype theory and the ENCODE results, which together suggest that much of this so-called “junk” DNA of ERV’s is functional.

[rsewell (RON SEWELL)]

@RTBsupporter

To clarify, our hypothesis about 80% of ERVs being functional arises from a synthesis of Owen’s archetype theory and the ENCODE results, which together suggest that much of this so-called “junk” DNA of ERV’s is functional.

Given that ERVs originated as genetic insertions from live viruses, all of that code was functional at one time.

[heymike3]

Dear Mac, thinking more about this, I thought you or someone you know with an interest in philosophy might be interested to consider a question I posed to the Biologos forum over 3 years ago:

@heymike3

Has anyone thought about how an uncaused cause would be unobservable by nature?

It is totally fascinating to me how an uncaused cause relates to conscious intention (to cause an action without being acted upon) and how this action of thought may or may not be located outside the body in the quantum realm.

At this stage of scientific discovery, there seems to be a remarkable parallel to solipsism. The further you go, the more subjective it becomes. Many years ago as a philosophy undergrad, I found the rational possibility of solipsism to be a very strong evidence that we are living in a fallen world.

And I never would have given it a moments thought, if I had not thought I could know God through a philosophical argument after my belief in Jesus was severely trashed by a Jesus mythicist.

Eventually the “therefore know for certain” and the 3 types of evidence that support it from Acts 2:14-36 were super helpful in settling some of those doubts for me.

I’m always interested in talking about this stuff, and would like to continue the conversation with someone from RTB. Hugh Ross was one of my main guys after I read the Genesis Question as a new believer 25 years ago.

Best Regards,
Mike

[RTBsupporter]

Did you get a chance to read section “Origin of Species model” of our article?

[jammycakes (James McKay)]

@RTBsupporter

At the time, I was specifically referring to endogenous retroviruses (ERVs), where the 80% functionality prediction remains unconfirmed. In contrast, the ENCODE project confirmed that 80% of junk DNA overall has functional activity. To clarify, our hypothesis about 80% of ERVs being functional arises from a synthesis of Owen’s archetype theory and the ENCODE results, which together suggest that much of this so-called “junk” DNA of ERV’s is functional.

Discussing whether or not ERVs are functional misses the point. It isn’t that they’re “junk”; it’s that they appear in exactly the same places in the respective genomes of different species.

[RTBsupporter]

@jammycakes

Discussing whether or not ERVs are functional misses the point. It isn’t that they’re “junk”; it’s that they appear in exactly the same places in the respective genomes of different species.

I apologize but what exactly is your point?

[heymike3]

I looked at it briefly and still lean strongly in favor of an OEC reading of Genesis 1 and 2. I haven’t yet been fully persuaded with Walton’s or Longman’s reading.

[heymike3]

Oh… you probably meant the question with respect to my comment

@heymike3

At this stage of scientific discovery, there seems to be a remarkable parallel to solipsism. The further you go, the more subjective it becomes.

It’s when you go beyond Genesis 1:1 where that starts to happen. Dt 29:29 comes to mind.

Quantum consciousness certainly touches on that boundary or this comment I stumbled on not too long ago:

“if the boundary condition is not objective for environmental decoherence then you have to talk about observer relative quantum states.”

Or Julian Barbour’s The Janus Point:

[St.Roymond]

@adamjedgar

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

Why? None of the people in the informal intelligent design club when I was in university included any biblical references in their conclusion of design; the place of biblical references is, having concluded there must be a Designer, to address the question, “Does this appear to be a communication from the Designer?”

[St.Roymond]

@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.

From my skim of the article it seems that expertise in metaphysics is also required, since that is where teleological arguments belong.

@RTBsupporter

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

The reference to software engineering was worth some laughs; the comparison would only work if coders regularly included and re-used large stretches of non-code text within programs that primarily consisted of chunks of older programs with no relation to the purpose of the one being written.

@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, too.

@RTBsupporter

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.

This sounds to me like hand-waving metaphysical mumbo-jumbo.

@T_aquaticus

@RTBsupporter

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.

That’s what I figured, but wasn’t sure enough to say it!

@pevaquark

Maybe the percentage could be figured out by how much an average computer programmer adds non-coding commentary to their code since that’s cited as evidence a divine creator would use nested hierarchies.

This brought up a memory: when my older brother was working for a computer company doing both software and hardware stuff, one of his coworkers was told by a boss that he wasn’t including enough commentary in his code. Suspecting that the boss wasn’t actually reading the code or commentary, in his next assignment he included commentary that, separated from useful commentary in different sections, said:

’Twas brillig, and the slithy toves
Did gyre and gimble in the wabe:
All mimsy were the borogoves,
And the mome raths outgrabe.

“Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
The frumious Bandersnatch!”

He took his vorpal sword in hand;
Long time the manxome foe he sought—
So rested he by the Tumtum tree
And stood awhile in thought.

And, as in uffish thought he stood,
The Jabberwock, with eyes of flame,
Came whiffling through the tulgey wood,
And burbled as it came!

One, two! One, two! And through and through
The vorpal blade went snicker-snack!
He left it dead, and with its head
He went galumphing back.

“And hast thou slain the Jabberwock?
Come to my arms, my beamish boy!
O frabjous day! Callooh! Callay!”
He chortled in his joy.

’Twas brillig, and the slithy toves
Did gyre and gimble in the wabe:
All mimsy were the borogoves,
And the mome raths outgrabe.

. . . with of course comments pointing to other comments showing in what order it should be read.

The only comment from the boss was approval of increased commentary!

Now if he’d only written it in a nested hierarchy form . . .

[St.Roymond]

@glipsnort

And then there’s the appeal to “baraminology”, which isn’t remotely science,

Where is that? I missed it on my skimming.

It’s not only not remotely science, it’s not remotely theology – to borrow a phrase from one of my grad school professors, it’s a bastard child of ignorance and wishful thinking.

@RTBsupporter

we demonstrate that scientists assume no conscious agent or designer is guiding mutations (i.e., no external teleology).

Of course they don’t – they’re doing science, not metaphysics.
And as I recall, randomness isn’t an assumption, it’s an observation.

@RTBsupporter

The question is why this designer would choose nested patterns to design organisms over other potential patterns.

How about, as was the common view in our informal university intelligent design club, because that’s how the system set u to run according to selected and established natural laws works?

I’m not confident I’m following all of this, but from what I do grasp it sounds to me like this paper is arguing in favor of the sort of view that when I was a university student drove people away from the Gospel.

@glipsnort

‘biochemically active’ does not imply ‘does something useful’.

That set me to laughing. The image that came to mind was the time that a load of gravel was delivered to a job site at the county fairgrounds one summer and the driver dumped it in a spot that just happened to be in the way of work to repair the horse barns. Since the grounds tractor was undergoing repairs, three of us got assigned to move the pile of gravel by hand – and then after the repair to the horse barns was finished we got to move it back. We were definitely active, but I can’t say that we were doing much that was useful!

[glipsnort (Steve Schaffner)]

@St.Roymond

Where is that? I missed it on my skimming.

In the section on testing their model.

[T_aquaticus (The Friendly Neighborhood Atheist)]

@RTBsupporter

You’re now asking for evidence supporting a specific mechanism. Currently, empirical evidence demonstrating this mechanism in living systems remains inconclusive.

Then the claims should be pulled from the paper until you have that evidence. You have no scientific reason to think the things happening with microtubules have anything to do with the production of mutations.

@RTBsupporter

We’re not claiming randomness in mutations in the way you’re interpreting it. Instead, we demonstrate that scientists assume no conscious agent or designer is guiding mutations (i.e., no external teleology). Our research challenges or questions that assumption, but this won’t be conclusive until scientists test and confirm the prediction I just mentioned.

Scientists make no such assumption. The data on mutations is already out there in the public domain. If you can’t show how the data supports your claims then it is a no go, and should be pulled from the paper. For example, you could start with the Luria and Delbruck paper and the Lederbergs’ paper which together form the earliest foundations of what are considered to be random mutations.

MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE

REPLICA PLATING AND INDIRECT SELECTION OF BACTERIAL MUTANTS

@RTBsupporter

I agree with you if you’re referring to internal teleology or functional elements related to fitness, or if you’re using the selection-effect definition of function. However, when we claim that the majority of junk DNA is functional, it’s in the context of external teleology and the causal role definition of function, as predicted by Owen’s theory.

The causal role is nonsense, so that’s a no go from the very start. It is equivalent to saying that you can smash a television into a million pieces and it will still be considered functional because it happens to bind a few dust particles from the air.

@RTBsupporter

We already understand why and how this designer produces nested patterns from Owen’s framework without depending on observations of human designers to gain insights.

Where in Owen’s framework does it state that a designer of life would necessarily produce a nested hierarchy? Don’t refer me to a large section of the paper. Quote from the paper where this is outlined.

@RTBsupporter

Since observations showing how the natural origin and design of viruses seem to mirror the artificial synthesis and design of viruses, it suggests this designer operates similarly to humans, we explored why human engineers use nested patterns and built a model from those insights, which is explained in the article.

That doesn’t mean anything. “Since observations showing how the natural origin and design of viruses seem to mirror the artificial synthesis and design of viruses” is empty rhetoric. It doesn’t describe any actual biology.

[RTBsupporter]

@T_aquaticus

Then the claims should be pulled from the paper until you have that evidence. You have no scientific reason to think the things happening with microtubules have anything to do with the production of mutations.

I said we did not have conclusive evidence, not that we have zero evidence. Here is the current evidence, though it’s not definitive since it doesn’t yet include viruses:

1. Sahu S., Ghosh S., Fujita D., Bandyopadhyay A. (2014). Live visualizations of single isolated tubulin protein self-assembly via tunneling current: effect of electromagnetic pumping during spontaneous growth of microtubule. Sci. Rep. 4:7303. [DOI] [PMC free article] [PubMed]

2. Slocombe L., Winokan M., Al-Khalili J., Sacchi M. (2023). Quantum tunneling effects in the guanine-thymine wobble misincorporation via tautomerism. J. Phys. Chem. Lett. 14, 9–15.

@T_aquaticus

Scientists make no such assumption.

That is certainly not what we have uncovered from the literature:

J.C. Avise, Colloquium paper: Footprints of nonsentient design inside the human genome. Proc. Natl Acad. Sci. U. S. A. 107 Supplement 2(supplement_2), 8969–8976 (2010).

F.J. Ayala, Darwin’s greatest discovery: Design without designer. Proc. Natl Acad. Sci. U. S. A. 104 (1) Supplement 1, 8567–8573 (2007).

@T_aquaticus

The causal role is nonsense, so that’s a no go from the very start. It is equivalent to saying that you can smash a television into a million pieces and it will still be considered functional because it happens to bind a few dust particles from the air.

As I told glipsnort@, Our model has different conditions and implications, which we explained in the subsection “Universal Common Designer.” I don’t see how what you’re saying is relevant to our approach.

@T_aquaticus

Where in Owen’s framework does it state that a designer of life would necessarily produce a nested hierarchy? Don’t refer me to a large section of the paper. Quote from the paper where this is outlined.

To clarify, the specific quote you’re asking for is located in the second and third paragraphs under the section titled “Reasons for choosing nested patterns.” You can refer directly to these paragraphs for the explanation and then you can copy and paste it here.

@T_aquaticus

That doesn’t mean anything. “Since observations showing how the natural origin and design of viruses seem to mirror the artificial synthesis and design of viruses” is empty rhetoric. It doesn’t describe any actual biology.

Let me be more specific. You previously stated that “The designs of human engineers don’t fall into a nested hierarchy.” However, we provided research showing how viruses both produce and mimic nested patterns. Additionally, viruses are utilized in synthetic biology for designing organisms, illustrating the parallels between natural and engineered patterns.

[T_aquaticus (The Friendly Neighborhood Atheist)]

@RTBsupporter

I said we did not have conclusive evidence, not that we have zero evidence. Here is the current evidence, though it’s not definitive since it doesn’t yet include viruses:

It’s two unrelated processes. Also, what is the deal with viruses? The vast, vast majority of mutations have nothing to do with viruses.

@RTBsupporter

That is certainly not what we have uncovered from the literature:

A few outliers does not a consensus make. The conclusion of random mutations is based on evidence, not on assumptions.

@RTBsupporter

As I told glipsnort@, Our model has different conditions and implications, which we explained in the subsection “Universal Common Designer.” I don’t see how what you’re saying is relevant to our approach.

Yet you never actually quote the paper where these are outlined. Why?

As I stated earlier, the causal role is nonsense. Just existing does not make a DNA sequence functional. Transcription is not function as we would expect non-functional DNA to be transcribed.

@RTBsupporter

To clarify, the specific quote you’re asking for is located in the second and third paragraphs under the section titled “Reasons for choosing nested patterns.”

Then quote it.

@RTBsupporter

However, we provided research showing how viruses both produce and mimic nested patterns. Additionally, viruses are utilized in synthetic biology for designing organisms, illustrating the parallels between natural and engineered patterns.

Again, what is it with viruses?

Just because humans use a naturally occurring virus does not make viruses part of a design.

[RTBsupporter]

@T_aquaticus

It’s two unrelated processes. Also, what is the deal with viruses? The vast, vast majority of mutations have nothing to do with viruses.

That reminds me to clarify something I mentioned earlier. Microtubules are not the biological mechanism of Owen’s extended theory itself, but rather the site or medium where quantum processes take place.

Quantum tunneling is an important phenomenon that occurs in both microtubules and during the process of mutations.

So, you’re correct—they are not directly related processes. However, I referenced those studies to illustrate how quantum tunneling plays a role in both microtubules and mutations.

@T_aquaticus

Yet you never actually quote the paper where these are outlined. Why?

I haven’t directly quoted the paper because I don’t want to flood the discussion with large excerpts. Instead, I encourage you to read the last two paragraphs under the subsection “Universal Common Designer.” Those sections explain why the causal role is essential and why it’s appropriate for assessing whether our model holds up.

@T_aquaticus

As I stated earlier, the causal role is nonsense. Just existing does not make a DNA sequence functional. Transcription is not function as we would expect non-functional DNA to be transcribed.

While transcription may not necessarily imply utility, it does imply necessity. This is particularly relevant to our theory, given the long-standing argument that a divine designer or God is not considered necessary or evident in biology. Our model challenges that view.

@T_aquaticus

A few outliers does not a consensus make. The conclusion of random mutations is based on evidence, not on assumptions.

Well, it all depends on which definition of function and random mutations you are using.

@T_aquaticus

Then quote it.

Again, I prefer not to copy and paste large sections of our article here. You can find the information you’re asking for in the second and third paragraphs under the section titled “Reasons for Choosing Nested Patterns.”

@T_aquaticus

Again, what is it with viruses?

Just because humans use a naturally occurring virus does not make viruses part of a design.

Our article provides a detailed explanation of this. Owen’s extended theory offers a plausible design-based explanation for viruses, supported by evidence from real-time experiments where humans replicate similar effects. This approach is based on Charles Lyell’s principle of causation, which suggests that explanations for past phenomena should rely on causes observed in our current experience to produce similar effects.

[heymike3]

@RTBsupporter

This approach is based on Charles Lyell’s principle of causation, which suggests that explanations for past phenomena should rely on causes observed in our current experience to produce similar effects.

Mac, I would like to encourage you to think more about the significance for the unobservability of an uncaused cause. I might not have said this already, but the immediate effect of an uncaused cause will appear to come from nothing. Which is interesting in that for any event that occurs, it can be asked if it was caused by another event to which the same question applies. The event can be considered to be uncaused and just happens. Or the event can be the immediate effect of something that doesn’t happen. The thing is all three descriptions can or will appear to come from nothing.

[RTBsupporter]

@heymike3

The thing is all three descriptions can or will appear to come from nothing.

Define nothing according to you.

[T_aquaticus (The Friendly Neighborhood Atheist)]

@RTBsupporter

So, you’re correct—they are not directly related processes. However, I referenced those studies to illustrate how quantum tunneling plays a role in both microtubules and mutations.

Quantum tunneling plays a role in a ton of biological and non-biological processes. How do you go from quantum tunneling to mutations are guided? Is each and every decay of an atomic nuclei also guided?

@RTBsupporter

While transcription may not necessarily imply utility, it does imply necessity.

No, it doesn’t. There is nothing about transcription that implies any piece of DNA in a genome is necessary. We fully expect a random and non-functional sequences of DNA to contain weak transcription factor binding sites that will drive low level transcription of non-functional DNA. We also expect RNA polymerases to bind off target from time to time, driving low level expression of non-functional DNA.

In the case of the ENCODE study, if there was just a single copy of an RNA transcript in one cell they counted the complementary DNA sequence to be “biologically active”. Such a low bar guarantees that “biologically active” DNA includes non-functional DNA.

@RTBsupporter

Well, it all depends on which definition of function and random mutations you are using.

Function = the sequence of bases in a stretch of DNA impacts the fitness of the organism

random mutations = the chances of a specific mutation occurring is not influenced by its impact on fitness

@RTBsupporter

Again, I prefer not to copy and paste large sections of our article here.

Then I can only conclude that the claims you are making in this thread are not supported by the paper.

[RTBsupporter]

@T_aquaticus

Quantum tunneling plays a role in a ton of biological and non-biological processes. How do you go from quantum tunneling to mutations are guided? Is each and every decay of an atomic nuclei also guided?

For a detailed explanation of how, Go to subsection " Human consciousness" of our article where we go in-depth about how.

@T_aquaticus

No, it doesn’t. There is nothing about transcription that implies any piece of DNA in a genome is necessary. We fully expect a random and non-functional sequences of DNA to contain weak transcription factor binding sites that will drive low level transcription of non-functional DNA. We also expect RNA polymerases to bind off target from time to time, driving low level expression of non-functional DNA.

In the case of the ENCODE study, if there was just a single copy of an RNA transcript in one cell they counted the complementary DNA sequence to be “biologically active”. Such a low bar guarantees that “biologically active” DNA includes non-functional DNA.

If most of the binding interactions were random, it would likely disrupt gene regulation, as random interactions between genome components could be highly detrimental to the organism. Without controlling these disruptive interactions, cellular biochemical processes would likely come to a standstill. This suggests that the majority of the binding measured in the ENCODE project was likely functional.

A study from Harvard researchers supports this idea, showing that the concentration of proteins involved in protein-protein interactions (PPIs) is also finely regulated:

Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions | PNAS

@T_aquaticus

Function = the sequence of bases in a stretch of DNA impacts the fitness of the organism

random mutations = the chances of a specific mutation occurring is not influenced by its impact on fitness

Awwwww, as I thought, As I said before, we are using a different definition of function and random to evaluate whether Owen’s theory holds up NOT Darwinian theory.

@T_aquaticus

Then I can only conclude that the claims you are making in this thread are not supported by the paper.

Why can’t you just copy and paste it yourself and I will confirm whether you copied the right information?