The Argument Clinic

[Meerkat_SK5]

@Dan_Eastwood

Because science is the same for everyone. If it were different, then it should be a simple matter to find evidence of that difference. That never happens.

I am not sure what you mean by that. For instance, Paleontologists would obviously not think this framework could lead to successful research for their work because it is not in their field of expertise.
So how could it be the same for everyone?

@John_Harshman

So you have no explanation, just a blind hope that in the future there will be. At present, though, it’s evidence against your notions.

@John_Harshman

Nothing to do with what you’re talking about except that it mentions wasps.

Several studies show how animal death and carnivorous activity play a necessary role in preventing an overpopulation of herbivores (and carnivores) that would potentially go extinct from starvation by eating all their food sources and the fixation of harmful mutations or pathogens within populations that would potentially cause the population to become extinct as well.

Predator control of ecosystem nutrient dynamics - Schmitz - 2010 - Ecology Letters - Wiley Online Library

Predators indirectly control vector-borne disease: linking predator–prey and host–pathogen models - PMC (nih.gov)

A400_5f 563…566 (elkhornsloughctp.org)

Adaptive rewiring aggravates the effects of species loss in ecosystems | Nature Communications

@John_Harshman

Not what you’re talking about. These are not separately created kinds. Saltations are big changes in existing groups. Further, the phenomenon of stasis and punctuation involves individual species, not the families and higher taxa you claim to be kinds.

I originally pointed out that a scientific theory is a large overarching explanation that is well-tested and unites lots of fields and explains lots of different kinds of observations. What springs forth from there are hypothesizes that are narrow and we can test it, such as my biochemical model of common design. This means that the same theory can be used by different scientists to make different predictions that are later confirmed through future experiments and observations.

What I was just trying to do before is show how Richard Owen’s universal common archetype from a Divine mind is a well-tested overarching theory. One of the reasons why it is well-tested and supported is because it predicted a saltational process for the origin of species and stasis followed by sudden appearances:

"Advocates of these views often do not completely deny gradual changes (typically during adaptation or microevolution), but consider them unable to explain the origin of phenotypic novelties, or species and higher order taxa. For the advocates of mutationism and saltationism, sudden and discontinuous changes appear to be required to explain the origin of profound phenotypic novelties or species "

Theissen2009.pdf (evolocus.com)

In contrast, my particular common design model is a hypothesize that makes new predictions, but still flows out of that overarching theory. The separate creation of orders and families is one of those new predictions.

@John_Harshman

The papers you cite do not support your claims.

From one of the studies I referenced already:

“The fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results.”

As I mentioned, Richard Owen’s theory involving a saltational process explains these “strikingly divergent results.”

Moreover, the new life-forms removed the just-right amounts of carbon dioxide and methane from the atmosphere to perfectly compensate for the brightening Sun:

“Our model calculations suggest that the lower albedo of the early Earth provided environmental conditions above the freezing point of water, thus alleviating the need for extreme greenhouse-gas concentrations to satisfy the faint early Sun paradox.”

@John_Harshman

Those are not “cognitive qualities”, and what makes you think that they would not be predicted under common descent? Doesn’t evolution result in new forms? Are these genes, or there orthologs, not also found in other species?

@T_aquaticus

Why wouldn’t we expect that from evolution and common descent?

@T_aquaticus

Why couldn’t evolution and common descent produce novel adaptations?

Our cognitive abilities come from our embryonic development and subsequent development after birth. That development is produced by our DNA. Can you show us any differences between our genomes and the genomes of other species that you claim couldn’t be produced by known evolutionary mechanisms and common descent?

This common designer implies having a common design rather than a common descent because only humans produce top-down causation in the form of algorithmic information or RNA viruses. More importantly, observations have suggested that viruses were not only the probable precursors of the first cells but also helped shape and build the genomes of all species, including humans. [36]

For instance, scientists synthesized the RNA molecules of a virus and reconstructed a virus particle from scratch. [37] They accomplished this by creating another virus and using its parts, such as specialized proteins (enzymes), to construct an RNA virus to solve the problem of an unstable RNA. Other experiments have shown that RNA viruses can be engineered to interact with the host miRNA pathways, and miRNAs can be used to control viral tropism. [38]

For example, endogenous retroviruses (ERVs) protect the host cell’s genome from retroviral infections by disrupting the endogenization process of invading retroviruses. ERVs must resemble retroviruses to act as a defense mechanism against incoming harmful viruses. [39]

A different study from Kazuaki Monde et al. also revealed that “the strict dependence of HERV-K on SOX-2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos.” [40]

This is how human designers operate. They use preexisting mechanisms, material parts, and digital information to assemble designs to achieve a purpose.

The other reason a common designer implies having a common design rather than a common descent is because natural selection lacks the capacity to elucidate the physical mechanisms underlying the transition from non-life to life or to distinguish non-living from living. [41]

Furthermore, RNA viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic—they have many evolutionary origins. [42]

Overall, this is why we can infer that all living animals share a common design that can be traced back to a universal common designer. If this theory is true, then we can expect humans to possess cognitive qualities that are exceptions to what would otherwise be predicted if we were evolutionary descendants.

[36] Are viruses our oldest ancestors? | EMBO reports (embopress.org)

[37] Cello, J., Paul, A.V. and Wimmer, E., 2002. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science, 297(5583), pp. 1016-1018.

https://www.science.org/content/article/poliovirus-baked-scratch

[38] Tenoever, B.R., 2013. RNA viruses and the host microRNA machinery. Nature Reviews Microbiology, 11(3), pp. 169-180.

https://www.nature.com/articles/nrmicro2971

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

[40] Movements of Ancient Human Endogenous Retroviruses Detected in SOX2-Expressing Cells | Journal of Virology (asm.org)

[41] The algorithmic origins of life | Journal of The Royal Society Interface (royalsocietypublishing.org)

[42] Ten reasons to exclude viruses from the tree of life | Nature Reviews Microbiology

Viruses and the tree of life (virology.ws)

@T_aquaticus

The mixture of features produces a nested hierarchy, a pattern that is only predicted by common descent.

Not true, common design or HRT can and does produce the same patterns:

A phylogenetic tree built from BovB sequences from species in all of these groups does not conform to expected evolutionary relationships of the species, and our analysis indicates that at least nine HT events are required to explain the observed topology. Our results provide compelling evidence for HT of genetic material that has transformed vertebrate genomes.

https://www.pnas.org/doi/abs/10.1073/pnas.1205856110

" we statistically tested for incongruence between the topology of the promoter sequences against the species tree. The null hypothesis of this test is vertical inheritance (as defined by the species tree); therefore, rejection of the null hypothesis is a strong indication of HRT. We found that 51% of all core gene promoters are incongruent with the species phylogeny, indicating that regulatory regions, similar to coding genes, are frequently transferred. " Transfer of noncoding DNA drives regulatory rewiring in bacteria | PNAS

“Because of the critical tasks of translation elongation factors, it is widely believed that EF-1α/EF-Tu genes have been vertically inherited from the last universal common ancestor (3–5), and the gene products are ubiquitous in all extant cells. However, large-scale sequence data from phylogenetically diverged organisms started unveiling cases that clearly violate the above preconception about EF-1α/EF-Tu evolution.”
Direct phylogenetic evidence for lateral transfer of elongation factor-like gene - PMC (nih.gov)

@T_aquaticus

Darwin himself predicted the punctuated nature of the fossil record:

Only a small portion of the world has been geologically explored. Only organic beings of certain classes can be preserved in a fossil condition, at least in any great number. Widely ranging species vary most, and varieties are often at first local, – both causes rendering the discovery of intermediate links less likely. Local varieties will not spread into other and distant regions until they are considerably modified and improved; and when they do spread, if discovered in a geological formation, they will appear as if suddenly created there, and will be simply classed as new species. [Charles Darwin, Origin of Species 1st Edition 1859, p.439]

A study by biologists demonstrated, at the molecular level, that evolution is both unpredictable and irreversible. [56] The study focused exclusively on the type of evolution known as purifying selection, which favors mutations with no or only a small effect in a fixed environment. This is in contrast to adaptation, in which mutations are selected if they increase an organism’s fitness in a new environment. Purifying selection is by far the more common type of selection.

[56] Shah, P., McCandlish, D.M. and Plotkin, J.B., 2015. Contingency and entrenchment in protein evolution under purifying selection. Proceedings of the National Academy of Sciences, 112(25), pp. E3226-E3235.

https://www.pnas.org/doi/full/10.1073/pnas.1412933112

Consequently, we would expect novelty or speciation to be extremely rare under common descent models. Second, occurrences of convergence where the environmental, predatory, and competitive selection effects would not at all be similar.

[T_aquaticus]

@Meerkat_SK5

This common designer implies having a common design rather than a common descent because only humans produce top-down causation in the form of algorithmic information or RNA viruses.

So why do me and my siblings have common designs? Isn’t it due to common descent?

Also, a nested hierarchy does not point to common design. it points to common descent. Human designs do not fall into a nested hierarchy. Common descent is the only process that we know of that necessarily produces a nested hierarchy.

@Meerkat_SK5

For example, endogenous retroviruses (ERVs) protect the host cell’s genome from retroviral infections by disrupting the endogenization process of invading retroviruses. ERVs must resemble retroviruses to act as a defense mechanism against incoming harmful viruses.

ERV’s protect against subsequent infection because they were once viruses. Transcripts from ERV’s bind to transcripts from the infecting retrovirus because of complementary sequence, and that complementary sequence is a result of previous insertion of a retrovirus into the host genome.

On top of that, only 10% of ERV’s have the necessary open reading frames to participate in this sort of viral protection, and of those only a tiny fraction have the necessary open reading frames for a given retrovirus. About 90% of ERV’s are just solo LTRs that lack the gag, env, and pol genes necessary. So it is very misleading to pretend as if all ERV’s serve this function. Nor is it required for different species to have the same ERV at the same orthologous base in each of their genomes in order to have this function. Only common descent can explain why we see a pattern of orthologous ERV’s.

@Meerkat_SK5

This is how human designers operate. They use preexisting mechanisms, material parts, and digital information to assemble designs to achieve a purpose.

That’s how common descent works. More importantly, common descent necessarily produces a nested hierarchy when there is vertical inheritance. Common design is not required to follow a nested hierarchy. What do we see? A nested hierarchy.

@Meerkat_SK5

Not true, common design or HRT can and does produce the same patterns:

No, it doesn’t. For example, cars don’t fall into a nested hierarchy. There is absolutely no design reason why life should fall into a nested hierarchy other than common descent.

@Meerkat_SK5

A study by biologists demonstrated, at the molecular level, that evolution is both unpredictable and irreversible. [56] The study focused exclusively on the type of evolution known as purifying selection, which favors mutations with no or only a small effect in a fixed environment. This is in contrast to adaptation, in which mutations are selected if they increase an organism’s fitness in a new environment. Purifying selection is by far the more common type of selection.

[56] Shah, P., McCandlish, D.M. and Plotkin, J.B., 2015. Contingency and entrenchment in protein evolution under purifying selection. Proceedings of the National Academy of Sciences, 112(25), pp. E3226-E3235.

https://www.pnas.org/doi/full/10.1073/pnas.1412933112

Consequently, we would expect novelty or speciation to be extremely rare under common descent models. Second, occurrences of convergence where the environmental, predatory, and competitive selection effects would not at all be similar.

It only needs to be rare in order to get novel adaptations.

[John_Harshman]

@Meerkat_SK5

Several studies show how animal death and carnivorous activity play a necessary role in preventing an overpopulation of herbivores (and carnivores) that would potentially go extinct from starvation by eating all their food sources and the fixation of harmful mutations or pathogens within populations that would potentially cause the population to become extinct as well.

Again, nothing to do with the parasitism of ichneumon wasps on caterpillars.

@Meerkat_SK5

What I was just trying to do before is show how Richard Owen’s universal common archetype from a Divine mind is a well-tested overarching theory.

You have done nothing to show this, and in the process you have presented incoherent claims, not tests.

@Meerkat_SK5

"Advocates of these views often do not completely deny gradual changes (typically during adaptation or microevolution), but consider them unable to explain the origin of phenotypic novelties, or species and higher order taxa. For the advocates of mutationism and saltationism, sudden and discontinuous changes appear to be required to explain the origin of profound phenotypic novelties or species "

That’s not Owen’s archetype theory, which has no necessary connection to saltationism; it’s just that Owen was also a saltationist. Note again that saltational transitions do not deny common descent. This is all your distortion. Also note that the fossil record shows missing transitions at the level of species, not higher taxa. And yet you claim that species within a kind share common descent while higher taxa do not, the opposite of what the fossils, naively interpreted, show.

@Meerkat_SK5

In contrast, my particular common design model is a hypothesize that makes new predictions, but still flows out of that overarching theory. The separate creation of orders and families is one of those new predictions.

And that’s a prediction falsified by the very fossil record you appeal to.

@Meerkat_SK5

From one of the studies I referenced already:

“The fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results.”

That has nothing whatsoever to do with your claims except that it includes a few of the same words. You really unerstand almost nothing of what you read, and that’s a problem.

@Meerkat_SK5

As I mentioned, Richard Owen’s theory involving a saltational process explains these “strikingly divergent results.”

It doesn’t, you know. It has nothing to do with those results.

@Meerkat_SK5

This common designer implies having a common design rather than a common descent because only humans produce top-down causation in the form of algorithmic information or RNA viruses.

That’s a non sequitur followed by more non sequiturs that claim to support it. This is hopeless.

[Dan_Eastwood]

@Meerkat_SK5

@Dan_Eastwood

Because science is the same for everyone. If it were different, then it should be a simple matter to find evidence of that difference. That never happens.

I am not sure what you mean by that.

This is evident. There have been many efforts to explain this to you, and you do not grasp the significance. Rather than repeat all that, I’ll take the Socratic approach:

HOW IT SCIENCE THE SAME FOR EVERYONE?

[Mercer (John Mercer)]

@Meerkat_SK5

For instance, Paleontologists would obviously not think this framework could lead to successful research for their work because it is not in their field of expertise.

For instance(s), I have moved between fields several times in my career, covering developmental biology, physiology, neuroscience, mouse genetics, cell biology, biochemistry, and cardiology. This idea that competent scientists are constrained is nonsense.

[Meerkat_SK5]

@T_aquaticus

So why do me and my siblings have common designs? Isn’t it due to common descent?

Let me first define it for you…

Common design: To create and develop animals through the common process of HGT for the common purpose of surviving, reproducing, and pioneering different environments.

Universal common designer: universal self-collapsing genetic code shown by the shared DNA among all living organisms (i.e., objective reduction).

Both common design and common descent are two different explanations that explain the same data, such as why you and your siblings have the same genes. However, they make different predictions and models.

@T_aquaticus

Also, a nested hierarchy does not point to common design. it points to common descent. Human designs do not fall into a nested hierarchy. Common descent is the only process that we know of that necessarily produces a nested hierarchy.

I have already showed you all the studies showing how HGT explains the same patterns

@T_aquaticus

So it is very misleading to pretend as if all ERV’s serve this function.

I am not pretending but predicting based on the model that 80% of ERV’s are functional.

@T_aquaticus

Nor is it required for different species to have the same ERV at the same orthologous base in each of their genomes in order to have this function. Only common descent can explain why we see a pattern of orthologous ERV’s.

Not true, God needs to use this common mechanism to carry out the same purposes.

For instance, a different study I gave you from Kazuaki Monde et al. also revealed that “the strict dependence of HERV-K on SOX-2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos.”

@T_aquaticus

That’s how common descent works. More importantly, common descent necessarily produces a nested hierarchy when there is vertical inheritance. Common design is not required to follow a nested hierarchy. What do we see? A nested hierarchy.

@T_aquaticus

No, it doesn’t. For example, cars don’t fall into a nested hierarchy. There is absolutely no design reason why life should fall into a nested hierarchy other than common descent.

Let me explain it this way then….

Every living creature on Earth uses the same code, in which DNA stores information using four nucleotide bases. The sequences of nucleotides encode information for constructing proteins from an alphabet of 20 amino acids. Why were these numbers chosen rather than some other numbers?

Patel showed how quantum search algorithms explain why these numbers were chosen. [22] To summarize, if the search processes involved in assembling DNA and proteins are to be as efficient as possible, the number of bases should be four, and the number of amino acids should be 20.

In other words, to address a common set of problems faced by organisms possessing different characteristics and living in different habitats, a single optimal solution must be employed. This means that if we replay the evolutionary history of life, it would lead to identical or nearly identical outcomes. An experiment has revealed that this quantum search algorithm is itself a fundamental property of nature. [23]

So there is a reason why life needed to be this way. If things were any different, we would not even be able to ask the question in the first place because we wouldn’t exist.

[22] [quant-ph/0002037] Quantum Algorithms and the Genetic Code

[23] [1908.11213] The Grover search as a naturally occurring phenomenon

@John_Harshman

Again, nothing to do with the parasitism of ichneumon wasps on caterpillars.

What do you mean. It has everything to do with them because wasps on caterpillars are displaying animal death and carnivorous activity.

@John_Harshman

That’s not Owen’s archetype theory, which has no necessary connection to saltationism; it’s just that Owen was also a saltationist. Note again that saltational transitions do not deny common descent.

Yes, it is part of his theory John and saltations does involve sudden and discontinuous changes as the article suggested above:

Owen was a pivotal figure in the emergence of the evolutionary view of life forms as indicated by fossils. He was a strong advocate of the notion that the paleontological record is progressive, arguing in an anonymous Quarterly Review (1851) critique of Charles Lyell’s steady-state view of the geological past that the succession of fossils through time shows a distinct development from lower to higher. For Owen, this progressive change was a process guided by divine purpose. He believed in an orthogenetic-saltational process of organic unfolding, driven by an inherent tendency to change, not by contingent, gradualist, and external forces such as natural selection.

The phenomenon of metagenesis provided Owen with a visualizing aid for his notion of evolution. In the booklet On Parthenogenesis, or the Successive Production of Procreating Individuals from a Single Ovum (1849), he described the phenomenon of alternating generations in the reproductive cycles of, for example, aphids, jellyfish, or flukeworms. Characteristic of such metagenetic cycles is that the individual generations can differ in form from each other as much as different species or even genera, families, and orders do.

@John_Harshman

Also note that the fossil record shows missing transitions at the level of species, not higher taxa. And yet you claim that species within a kind share common descent while higher taxa do not, the opposite of what the fossils, naively interpreted, show.

No, my model claims species within a kind share common descent genetically or biochemically and It does not make specific predictions about the fossil record.

@John_Harshman

@Meerkat_SK5

In contrast, my particular common design model is a hypothesize that makes new predictions, but still flows out of that overarching theory. The separate creation of orders and families is one of those new predictions.

And that’s a prediction falsified by the very fossil record you appeal to.

We actually don’t know whether this is true yet according to the common design model. For further research, evolutionary biologists, paleontologists, ecologists, and molecular biologist will need to look for morpho-molecular dissimilarities and/or lack of fossil intermediates among order and family level taxa. Then, they need to use the two-step ecology criteria I described to confidently conclude common design, which would suggest they evolved separately .

@John_Harshman

That has nothing whatsoever to do with your claims except that it includes a few of the same words. You really unerstand almost nothing of what you read, and that’s a problem.

@John_Harshman

@Meerkat_SK5

As I mentioned, Richard Owen’s theory involving a saltational process explains these “strikingly divergent results.”

It doesn’t, you know. It has nothing to do with those results.

I am going to have to rely on Hugh Ross to explain it to you better then:

A fundamental tenet of all naturalistic models for the history of Earth’s life is that natural changes in the genomes of life will be responsible for the observed changes in the physical body structures (morphology) of life. Consequently, evolutionary trees developed from the observed patterns in present-day genomes and the presumed natural rates of change of those genomes (molecular clocks). Assuming that strictly materialistic processes are responsible for the changes occurring throughout the history of life, the phylogenetic trees should match the morphological changes and the timing of those changes observed in the fossil record .

The same kind of match between the paleontology and phylogenetics can be realized if God intervened throughout life’s history. However, apparently only supernatural interventions can explain significant mismatches between phylogenetic and paleontological trees.

@John_Harshman

@Meerkat_SK5

As I mentioned, Richard Owen’s theory involving a saltational process explains these “strikingly divergent results.”

It doesn’t, you know. It has nothing to do with those results

No evolutionary change punctuated by rapid biological innovations matches the patterns predicted if a common design/archetype accounts for life’s history and diversity.

This is because instances of high gene-tree conflict (discordance in phylogenetic signals across genes) in mammals, birds, and several major plant clades correspond to increased rates of morphological innovation.

@John_Harshman

That’s a non sequitur followed by more non sequiturs that claim to support it. This is hopeless.

You are conflating deductive reasoning with inductive ; yet scientific investigations rely on induction, not deduction. There is nothing wrong with concluding, when using inductive reasoning, that the designer is probably human because I am making use of induction (as do all scientists), not deduction.

@Dan_Eastwood

This is evident. There have been many efforts to explain this to you, and you do not grasp the significance. Rather than repeat all that, I’ll take the Socratic approach:

HOW IT SCIENCE THE SAME FOR EVERYONE?

Then, all I can say is that you are wrong. There are researchers on this forum that do think the framework can lead to successful research:

@colewd

@Meerkat_SK5

I don’t view them as the same kind, but two separate created kinds.

Ok so how did you determine this? If you can generate a reasonable standard for determining this that would be a huge step forward.

@Winston Ewert: The Dependency Graph of Life

An interesting and signficant article was published at the Discovery Institute, by @Winston_Ewert : The Dependency Graph of Life, DOI: 10.5048/BIO-C.2018.3. [NOTE: This thread has special rules; read and follow them or there will be consequences] This article is being drummed up by a past interlocutor of @vjtorley and myself (@Cornelius_Hunter) here on this forum thread: It has always been known that the common descent model fails, both from a long list of particular examples, as well as in systematic studies. But what might a better model be? Winston Ewert’s new paper (Ewert 11) presents a dependency graph model, inspired by computer science. The paper uses model selection methods, and shows that the dependency graph model is a far superior model compared to common descent. New Paper Demonstrates Superiority of Design Model - Scientific Evidence - The BioLogos Forum I thought it would be worth discussing this in …

@Mercer

For instance(s), I have moved between fields several times in my career, covering developmental biology, physiology, neuroscience, mouse genetics, cell biology, biochemistry, and cardiology. This idea that competent scientists are constrained is nonsense.

No no no, I did not mean it like that. I mean it is not going to appeal to Christian researchers for emotionally reasons NOT intellectual ones. They would be constrained by how much passion they may have for a particular subject within that field of expertise over another. This is why science cannot be the same for everyone. We all have particular biases that drive us to a particular subject within a field. But, intellectual reasons would play a part in it as well.

[Mercer (John Mercer)]

@Meerkat_SK5

Both common design and common descent are two different explanations that explain the same data,

No, they do not. The same designer uses different components. Designers are not constrained.

@Meerkat_SK5

I have already showed you all the studies showing how HGT does produce the same patterns

No, they do not show that.

@Meerkat_SK5

I am not pretending but predicting based on the model that 80% of ERV’s are functional.

What mechanism in your model predicts 80%?

@Meerkat_SK5

Not true, God needs to use this common mechanism to carry out the same purposes.

Who are you to decide what God does or does not need?

@Meerkat_SK5

Every living creature on Earth uses the same code, in which DNA stores information using four nucleotide bases.

Objectively false. There are differences in the genetic code, if that is what you are referring to.

@Meerkat_SK5

The sequences of nucleotides encode information for constructing proteins from an alphabet of 20 amino acids.

1. The sequences of nucleotides also encode functional RNAs. Why do you omit them?
2. There are many more than 20 amino-acid residues in proteins. Why? Did the Designer mess up?

@Meerkat_SK5

In other words, to address a common set of problems faced by organisms possessing different characteristics and living in different habitats, a single optimal solution must be employed.

In other words, both of your premises are false, so your conclusion is not supported.

[Mercer (John Mercer)]

@Meerkat_SK5

@Mercer

For instance(s), I have moved between fields several times in my career, covering developmental biology, physiology, neuroscience, mouse genetics, cell biology, biochemistry, and cardiology. This idea that competent scientists are constrained is nonsense.

No no no, I did not mean it like that. I mean it is not going to appeal to Christian researchers for emotionally reasons NOT intellectual ones.

Who are you to speak for Christian researchers like me? Given your lack of understanding of basic biology, your claim to know what appeals to real scientists is absurd.

@Meerkat_SK5

They would be constrained by how much passion they may have for a particular subject within that field of expertise over another.

The point, which like most sailed far over your head, is that we are not constrained by particular subjects.

@Meerkat_SK5

We all have particular biases that drive us to a particular subject within a field.

Real scientists are easily diverted by interesting questions, regardless of subjects and fields.

Please stop. You simply don’t know what you are talking about.

[John_Harshman]

@Meerkat_SK5

What do you mean. It has everything to do with them because wasps on caterpillars are displaying animal death and carnivorous activity.

Note that you cited a paper on ichneumon wasps that had nothing to do with carnivorous activity. And Darwin’s point about the wasps wasn’t about predation, per se, but about the cruel details of the particular form of predation.

@Meerkat_SK5

Yes, it is part of his theory John and saltations does involve sudden and discontinuous changes as the article suggested above:

I repeat: Owen believed in archetypes, and Owen was a saltationist, but those two ideas are not in any way connected. Neither follows from the other. Also, sudden changes presuppose common descent, which you deny. Your repeated quote says nothing relevant to your claims.

@Meerkat_SK5

No, my model claims species within a kind share common descent genetically or biochemically and It does not make specific predictions about the fossil record.

If it makes no predictions about the fossil record, what have you been blathering about all this time?

@Meerkat_SK5

We actually don’t know whether this is true yet according to the common design model.

Yes we do. There’s abundant evidence for the common descent of different orders and families. What you say hasn’t been looked at has indeed been looked at. Nor does similarity of ecology imply common design rather than common descent. Your criterion is worthless.

@Meerkat_SK5

I am going to have to rely on Hugh Ross to explain it to you better then:

Sorry, but Hugh makes no sense. He has no clue what he’s talking about there. In fact supernatural intervention explains nothing, because it just supposes that “God made it that way because he wanted to”, with no expectation of what would or would not be observed.

@Meerkat_SK5

No evolutionary change punctuated by rapid biological innovations matches the patterns predicted if a common design/archetype accounts for life’s history and diversity.

You have already (above) said that your model “does not make specific predictions about the fossil record”. Which is true? Prediction or no prediction? And again you fail to confront the actual pattern, stasis and punctuation within species but not between higher taxa, and it’s the latter your notions demand.

@Meerkat_SK5

This is because instances of high gene-tree conflict (discordance in phylogenetic signals across genes) in mammals, birds, and several major plant clades correspond to increased rates of morphological innovation.

I see no evidence of such a thing. Nor does that seem relevant to your model, such as it is. Now, what high amounts of gene-tree conflict result from bursts of speciation, i.e. many splitting events in an evolutionarily short time, the sort of thing expected from an adaptive radiation. And an adaptive radiation might also result in considerable morphological evolution. But the two are not otherwise connected.

@Meerkat_SK5

You are conflating deductive reasoning with inductive ; yet scientific investigations rely on induction, not deduction.

I am not. Inductive reasoning relies on the evidence to support an argument being a unique expectation of the hypothetis being supported. But you present irrelevance. Nothing you present as evidence ever actually supports what you claim, and most often it has no relation at all except for a few of the same words.

[John_Harshman]

@Meerkat_SK5

Patel showed how quantum search algorithms explain why these numbers were chosen. [22] To summarize, if the search processes involved in assembling DNA and proteins are to be as efficient as possible, the number of bases should be four, and the number of amino acids should be 20.

I will confess that I don’t understand this at all. Why wouldn’t 25 or 30 or 40 amino acids work as well?

[Tim]

@Meerkat_SK5

Universal common designer: universal self-collapsing genetic code shown by the shared DNA among all living organisms (i.e., objective reduction).

Balderdash!

Shear mangled, incoherent, ignorant, meaningless nonsense!

The phrase “universal self-collapsing genetic code” is simply the meaningless word salad that comes from juxtaposing lack of meaningful understanding of quantum physics with lack of meaningful understanding of genetics. The suggestion that this non-existent “universal self-collapsing genetic code” could be a “Universal common designer” is ludicrous.

Kindly stop wasting our time with this ignorant drivel!

Tim’s Universal “Universal” Theory

Any time @Meerkat_SK5 uses the word “universal” in a statement, it will have no scientific substantiation.
Examples:

• Universal common designer
• Universal self-collapsing genetic code
• Universal proto-consciousness field

[Tim]

By way of an experiment, I asked ChatGPT “What is a universal proto-consciousness field?” and got the reply:

The concept of a universal proto-consciousness field is a theory that suggests that there exists a fundamental field of consciousness that pervades the entire universe and serves as the source of all individual conscious experiences. This idea is often associated with spiritual and philosophical beliefs, but it has not been scientifically proven and is not widely accepted within mainstream science. The notion of a universal consciousness field remains largely a matter of speculation and is not supported by empirical evidence.

“What is a universal self-collapsing genetic code?”

I’m sorry, but I’m not familiar with the term “universal self-collapsing genetic code.” It doesn’t seem to be a well-established or widely used term in science. It’s possible that it refers to a theoretical or speculative idea that has not yet been validated by scientific research, or it could be a term used in a specific subfield or discipline that I am not familiar with.

In general, genetic code refers to the way in which DNA or RNA molecules encode the instructions for making proteins, which are the building blocks of life. The genetic code is considered to be universal in that it is nearly the same in all living organisms, from bacteria to humans. However, I have not come across the term “self-collapsing genetic code” in my training data.

“Do quantum search algorithms explain why there are four bases and 20 amino acids in genetics?”

Quantum search algorithms, which are based on quantum mechanics principles, can be used to search through large data sets much faster than classical algorithms. However, they do not explain why there are four bases and 20 amino acids in genetics.

The number of bases and amino acids in genetics is a result of the specific biochemistry and evolution of life on Earth. The four nitrogenous bases in DNA (adenine, guanine, cytosine, and thymine) were chosen because they can hydrogen bond with each other in a specific way to form the double-stranded DNA helix. The 20 common amino acids in proteins were selected through evolution because they are able to form a variety of structures and perform a wide range of functions.

In summary, the number of bases and amino acids in genetics is not related to quantum search algorithms, but rather to the biochemistry and evolution of life on Earth.

[Roy (30-year veteran)]

@Meerkat_SK5

Let me explain it this way then….

Every living creature on Earth uses the same code, in which DNA stores information using four nucleotide bases.

This is not true.

The sequences of nucleotides encode information for constructing proteins from an alphabet of 20 amino acids.

This is not entirely true.

Why were these numbers chosen rather than some other numbers?

This assumes that they were chosen, which does not appear to be the case.

Patel showed how quantum search algorithms explain why these numbers were chosen. [22] To summarize, if the search processes involved in assembling DNA and proteins are to be as efficient as possible, the number of bases should be four, and the number of amino acids should be 20.

Patel’s article must be about as useful as one that explains why elephants can fly.

[Meerkat_SK5]

@Mercer

No, they do not. The same designer uses different components. Designers are not constrained.

Now, I am pretty confident you did not read much of my paper. I will have to summarize a part of it then:

DNA contains two types of information: digital, represented by genetic information, and analog, represented by the genome; both are present in DNA and have many properties almost identical to those in man-made computers and linguistic texts.

Based on this data, God probably operated in a similar manner to humans when designing life on Earth. This means that we would not have to worry about using an unfalsifiable theory that involves an omnipotent human because a non-computable being like God cannot violate his own nature.

In other words, the non-computable trait that this designer possesses offsets the omnipotent trait that this designer would also have to possess if this is true. For this reason, we would expect God’s human nature to be consistent without the flaws that humans naturally have because of their inherent physical limitations.

This allows us to treat an omnipotent God in the same way we would treat other intelligent agents (Neanderthals, modern humans, extraterrestrial intelligence, etc.) when we want to use a valid cause to explain a biological phenomenon over a mindless force.

Thus, all candidates are considered natural but immaterial causes that we can test because consciousness is supposed to be fundamental physics not classical physics.

@Mercer

@Meerkat_SK5

I have already showed you all the studies showing how HGT does produce the same patterns

No, they do not show that.

Let me refresh your memory again then:

“Organisms that frequently exchange genes become more similar, and transfers between these groups may then be categorized as HGTs with a bias reflecting overall relatedness, even though the initial transfers may have been biased by other factors. We have previously shown that biased gene transfer CAN CREATE and maintain phylogenetic patterns that resemble the signal created through vertical inheritance .” [emphasis added]

Biased gene transfer and its implications for the concept of lineage (nih.gov)

@Mercer

What mechanism in your model predicts 80%?

Horizontal regulatory transfer (HRT)

@Mercer

Who are you to decide what God does or does not need?

@Mercer

Objectively false. There are differences in the genetic code, if that is what you are referring to.

I seriously doubt this is what I was referring to because I don’t even know what you are talking about. You are going to have to elaborate on your point because I rather not guess.

@Mercer

• The sequences of nucleotides also encode functional RNAs. Why do you omit them?
• There are many more than 20 amino-acid residues in proteins. Why? Did the Designer mess up?

Again, I’m not following you. What is your point? What are you getting at? What does this have to do with what I was explaining to @T_aquaticus? Or do you not understand the point I was making to him?

@Mercer

The point, which like most sailed far over your head, is that we are not constrained by particular subjects.

Actually, I was not trying to make a point or claim, but was trying to understand @Dan_Eastwood’s point better by inquiring more information when I said…

You mean no atheistic researchers would think it has any worth. But, what makes you think Christian researchers would feel the same way?

Then, I said…
I am not sure what you mean by that. For instance, Paleontologists would obviously not think this framework could lead to successful research for their work because it is not in their field of expertise.
So how could it be the same for everyone?

Also, when I asked these questions, I was referring to the emotional side of it, primarily.

@John_Harshman

Note that you cited a paper on ichneumon wasps that had nothing to do with carnivorous activity.

Sorry, I gave you the wrong study:

pnas.org/doi/10.1073/pnas.1115133109

@John_Harshman

And Darwin’s point about the wasps wasn’t about predation, per se, but about the cruel details of the particular form of predation.

That’s more of an aesthetics argument against it not a scientific one.

@John_Harshman

Owen believed in archetypes, and Owen was a saltationist, but those two ideas are not in any way connected. Neither follows from the other.

But you suggested that saltations theory is not part of his archetype theory, which is false. And I never said one follows from the other. Instead, I am saying Richard Owen put the two ideas together in his theory:

"Owen’s Platonism, as we have seen, is fully compatible with Cuvier’s fragmentation of the Great Chain of Being into diverse “embranchments,” placing new emphasis on individual species. Upon this structure, Owen was able to superimpose his theory of archetypes and other modifications which had been formulated to explain the lacunae in the chain’s continuity [7].

Owen explained that each section of the chain had its own archetype and does not have to be temporally complete. Certain intermediate species may exist either in the past or the future: ‘The possible and conceivable modifications of the vertebrate Archetype are far from having been exhausted in the forms that have hitherto been recognized, from the primaeval fishes of the Paleozoic ocean of this planet up to the present time.’

https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.923.6553&rep=rep1&type=pdf

@John_Harshman

Yes we do. There’s abundant evidence for the common descent of different orders and families. What you say hasn’t been looked at has indeed been looked at.

Yes, based upon your model and methods. But, based on our model and methods, we have a lot of preliminary results suggesting that many different orders and families evolved separately:

A List and Bibliography of Identified Baramins | Journal of Creation Theology and Science Series B: Life Sciences (coresci.org)

@John_Harshman

Nor does similarity of ecology imply common design rather than common descent. Your criterion is worthless.

No, this is not the ecology criteria I described before anymore. I made many changes to the method. Let me describe it to you again:

We can assess the prediction by applying analogous phenotypic traits between families and orders to different environmental niches based on similar needs.

There is a four-question survey where each practical criterion is designated by a letter (A–D) and a title in the form of a question (relating to food, predators, reproduction, and habitat).

For example, if the answer to the question “Is the common feature of this group being used differently in their habitats?” is “No,” “To be determined (TBD)," or “Not applicable (N/A),” a follow-up question is asked: “Do they respond differently in different habitats?” This may require artificially planting them in different habitats for an answer. If the answer to either question is “Yes,” we can start testing whether there are adaptive and structural convergent genes pertaining to the application of this analogous trait. If the test reveals at least one adaptive and/or structural gene, we can confidently conclude a common design.

However, if the answer to both questions is “No” or “TBD,” we must apply the same question formula to prey and/or predator measures to potentially draw a definite conclusion. If the answer is still “No” or “TBD,” then we ask, “Is the common feature of this group being used differently in sexual reproduction?”

The results are inconclusive if every question yields a “No” or “TBD” answer. This method was inspired by a study on red and giant pandas, which concluded that their false thumbs evolved separately in response to similar needs, [50] and a study that showed why and how they evolved separately. [51]

[50] Evidence of a false thumb in a fossil carnivore clarifies the evolution of pandas | PNAS

[51] Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas | PNAS

@John_Harshman

Sorry, but Hugh makes no sense. He has no clue what he’s talking about there. In fact supernatural intervention explains nothing, because it just supposes that “God made it that way because he wanted to”, with no expectation of what would or would not be observed.

Hugh ross is an advocate of Richard Owen’s theory. So “supernatural intervention” to him is just considered to be saltations theory.

@John_Harshman

You have already (above) said that your model “does not make specific predictions about the fossil record”. Which is true? Prediction or no prediction? And again you fail to confront the actual pattern, stasis and punctuation within species but not between higher taxa, and it’s the latter your notions demand.

@John_Harshman

I see no evidence of such a thing. Nor does that seem relevant to your model, such as it is. Now, what high amounts of gene-tree conflict result from bursts of speciation, i.e. many splitting events in an evolutionarily short time, the sort of thing expected from an adaptive radiation.

Yes, my model and predictions ,which are emanating from Richard Owen’s theory, does not . But, Richard Owen’s saltations model of the fossil record does, which he combined with his archetype theory. Just read the first 9 pages of this article, which he created after his archetype theory. It describes these splitting events in more detail:

On Parthenogenesis; Or, The Successive Production of Procreating Individuals … - Richard Owen - Google Books

@John_Harshman

I am not. Inductive reasoning relies on the evidence to support an argument being a unique expectation of the hypothetis being supported. But you present irrelevance. Nothing you present as evidence ever actually supports what you claim, and most often it has no relation at all except for a few of the same words.

That is because you did not read my entire article. I was merely copying and pasting what I wrote in my article. You should just read the rest of the article so you can better understand the context of what I was trying to convey.

@John_Harshman

I will confess that I don’t understand this at all. Why wouldn’t 25 or 30 or 40 amino acids work as well?

It looks like this article explains why…

Why twenty amino acid residue types suffice(d) to support all living systems - PMC (nih.gov)

[AllenWitmerMiller (Retired Professor & Minister.)]

@Tim

Shear mangled, incoherent, ignorant, meaningless nonsense!

I’m willing to call it: Byers’ Point™ reached.

[Tim]

@AllenWitmerMiller

I’m willing to call it: Byer’s Point™ reached.

Is there a formal definition of your “Byer’s Point”? Or is it merely the point at which the resemblance to Robert Byers becomes obvious. (Also, shouldn’t it therefore be “Byers’ Point”? )

[AllenWitmerMiller (Retired Professor & Minister.)]

The Byers’ Point™ is the point at which the absurdity of a position has gone hopelessly off the rails and all efforts of restoration to the realm of reason are futile. Yes, I coined it in honor of the allegedly indomitable Robert Byers when he was still frequenting PS.

@Tim

(Also, shouldn’t it therefore be “Byers’ Point”? )

Indeed it should. Unfortunately, I was using a junky bluetooth portable keyboard with an Android tablet and the keys alternate between not working and repeating, so I constantly have to backspace to try to edit what I just typed.

[John_Harshman]

@Meerkat_SK5

Sorry, I gave you the wrong study:

That was no different from your ordinary practice. And the “right” study is also irrelevant to the point.

@Meerkat_SK5

That’s more of an aesthetics argument against it not a scientific one.

Of course it isn’t a scientific argument. It’s a moral argument. Either God didn’t cause this, or God is cruel and immoral. Which would you prefer?

@Meerkat_SK5

But you suggested that saltations theory is not part of his archetype theory, which is false.

What evidence do you have that it’s false? As usual, what you quote and cite doesn’t say what you think it does.

@Meerkat_SK5

But, based on our model and methods, we have a lot of preliminary results suggesting that many different orders and families evolved separately:

Again, what you cite doesn’t say what you think or support what you claim.

@Meerkat_SK5

There is a four-question survey where each practical criterion is designated by a letter (A–D) and a title in the form of a question (relating to food, predators, reproduction, and habitat).

Much too vague, so much as to be non-operational. Further, there is no attempt to justify the criteria as delimiting a kind or basic type or whatever you think you’re talking about.

@Meerkat_SK5

Hugh ross is an advocate of Richard Owen’s theory. So “supernatural intervention” to him is just considered to be saltations theory.

Nope. Hugh Ross, last time he said anything, thought that every species was a separate creation. No saltation; that requires common descent.

@Meerkat_SK5

Yes, my model and predictions ,which are emanating from Richard Owen’s theory, does not .

You have no model. You have no predictions. And your understanding of Owen’s views is poor. And “does not” what?

@Meerkat_SK5

It describes these splitting events in more detail:

What “splitting events”?

@Meerkat_SK5

I was merely copying and pasting what I wrote in my article.

You should stop doing that over and over. Now, in a scientific paper, a reference is supposed to support the statement in which it is cited. “The rest of the article” is not relevant.

@Meerkat_SK5

It looks like this article explains why…

Not really, and it appears to be a completely different explanation from what’s hinted at in your previous source.

[Faizal_Ali]

@AllenWitmerMiller

I’m willing to call it: Byers’ Point™ reached.

But Byers, at least, managed to get his article published somewhere.

Post-Flood Marsupial Migration Explained – Revolution Against Evolution (rae.org)

[Meerkat_SK5]

@John_Harshman

And the “right” study is also irrelevant to the point

How so?

@John_Harshman

Of course it isn’t a scientific argument. It’s a moral argument. Either God didn’t cause this, or God is cruel and immoral. Which would you prefer?

No, aesthetic and moral values are not same thing:

Many philosophers, beginning with Plato, have classified aesthetic and
moral judgments together on the basis of one important, shared feature: both
involve value judgments. This practice is misleading, as these two forms of
judgment can be very different; for instance, moral judgments always imply
obligation and the compulsion to act in certain ways, features that are not
necessarily present in aesthetic judgments.
Microsoft Word - KAJH art 2-edited.doc (usm.my)

With that said, what about that act is considered to be immoral to you? It can’t be the death or pain part, is it?

@John_Harshman

What evidence do you have that it’s false? As usual, what you quote and cite doesn’t say what you think it does.

I will just go back to the same article, but this time I will only show you furhter details and highlights in it that should hopefully show you why you are grossly mistaken here:

He was a strong advocate of the notion that the paleontological record is progressive… For Owen, this progressive change was a process guided by divine purpose. He believed in an orthogenetic-saltational process of organic unfolding, driven by an inherent tendency to change…

The phenomenon of metagenesis provided Owen with a visualizing aid for his notion of evolution. In the booklet On Parthenogenesis, or the Successive Production of Procreating Individuals from a Single Ovum (1849), he described the phenomenon of alternating generations in the reproductive cycles of, for example, aphids, jellyfish, or flukeworms. …One could imagine that under particular circumstances the cycle might be broken, and the separate stages go on reproducing. In this way wholly new species might originate.

Owen applied his saltational theory of the origin of species also to humans and stressed the unity of mankind and the gap that exists between humans and the higher apes. Based on a series of comparative studies of the anthropoid apes, he placed humans in a subclass of their own, the Archencephala , pointing to a number of specific cerebral features, in particular the hippocampus minor .

@John_Harshman

Much too vague, so much as to be non-operational. Further, there is no attempt to justify the criteria as delimiting a kind or basic type or whatever you think you’re talking about.

This method was inspired by a study on red and giant pandas, which concluded that their false thumbs evolved separately in response to similar needs, and a study that showed why and how they evolved separately.

So the two-step ecology criteria are operational and validated by previous studies. I am merely combining the methods from each study into one.

@John_Harshman

You have no model. You have no predictions.

Origin of life and species model

Approximately 3.8 billion years ago, pi electron resonance clouds in single-chain amphiphile molecules coalesced in geometric pi-stacks, forming viroids with quantum-friendly regions for OR events within Earth’s deep-sea hypothermal vents. [45]

Subsequently, through natural selection and OR events, groups of viroids formed into highly ordered local domains of key biomolecules of a DNA/RNA virus or molecule, which later evolved into different species of unicellular organisms. [46]

Through HRT, these unicellular organisms underwent extensive regulatory switching and rewiring in their noncoding regulatory regions, which led to the divergence of transcription start sites and gene expression levels in the formation of primitive multicellular organisms. This same multicellular toolkit and modules of slime molds then developed into created kinds at different times and global locations (for more details, read Stuart Hammeroff’s description of how microtubules played a part in the origin of species). [5]

Origin of species predictions

Based on this theory, we would expect to find:

(A) Over 80% of families and orders evolved separately.

(B) Over 80% of ERVs and pseudogenes are functional.

(C) The regulatory regions of core gene promoters between families and orders are over 50% incongruent with species phylogenies (i.e., vertical inheritance).