Got my 
ready for the response.
I have decided to redo my model in a way that is hopefully more clear:
Around 3.8 billion years ago, there was a virus population that contained all the required genes to make certain evolutionary trajectories more likely.
Through natural selection, these viruses evolved into different unicellular species in the deep-sea hypothermal vents of the primitive earth, undergoing an extensive amount of HGT.
Subsequently, the designer re-used microbial parts and chemical consitutents to develop basic types with cytosine deanimation from different times and global locations. Through natural selection and HGT, these basic types would branch into diverse progeny to deliberately pioneer environments worldwide over long epochs.
No, the real issue is that you seem to be incapable of separating the concept of common descent and nested hierarchy. They are not synonymous. You keep imposing common descent onto those patterns. The HGT and common blueprint the designer used is what produces those same patterns WITHOUT violating them. But, this would still produce basic types separately because it used non-random mutations as well.
Because the genetic code is optimal and can handle it. While the cell is âfixing the buttons,â the DNA has more time to mutate. Thus, these repeats influence the mutation rate, as mutations in the repeats on either side of the mutated DNA would abrogate protein function, preventing them from being eliminated and resulting in a mutational hot spot in between stable DNA sequences.
Humans are contingent beings. God is a human as well BUT non-contingent, which means he is immutable and perfect. He cannot violate his own nature and will because it is logically impossible.
Because HGT can create nested hierarchies the same way that vertical inheritance can. More importantly, HGT has played a fundamental role in shaping the genomes of unicelluar and multicellular organisms. This means that we would expect to see a universal nested pattern from top to bottom.
No, actually. But, I can point to experiments that can show the universe and life is not designed.
According to the study I gave you, we do see the same genes move between the same species, which produce variety:
"Mobile genetic elements, including transposons, plasmids, bacteriophage and self-splicing molecular parasites, have played a crucial role in facilitating the movement of genetic material between organisms [7,8]. These elements likely already played a similar role in the early stages of lifeâs evolution [9], and continue to play a role even in multicellular eukaryotes.
For example, pervasive transfer of rolling-circle transposons (also called helitrons; [10]) has been reported to occur in many species of insects, plants and vertebrates, primarily through insect viruses as vectors [11]. During transposition, helitrons often capture genes or gene fragments from their host, and can therefore significantly influence the evolution of their host genome, for example through modifications of the transcriptome and in generating new genes [12]. These parasitic entities have been implicated in altering structural, functional and epigenetic variability of their host genome [13], consequently enhancing the evolvability of species and lineages." [emphasis added]
Functional but similar ERVâs found indepenedently in different organisms
Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach | PLOS Computational Biology
Non-functional binding sites are rare though. So this is very likely.
Right, but not anymore though because of the ENCODE project results. So we can view them as beneficial as well, which means a vast majority of mutations are now considered to be oriented to benefit the organism.
This is why mutations no longer should be considered random.
Since vast majority of mutations are oriented to benefit the organism from what was found in the ENCODE resultsâŚ
Mutations should no longer be considered random.
Oh yes it can explain the similarities, differences, AND nested patterns because HGT can create nested hierarchies that mimic patterns of vertical inheritance. More importantly, HGT has played a fundamental role in shaping the genomes of unicelluar and multicellular organisms. This means that we would expect to see a universal nested pattern from top to bottom without having to assume common descent.
No, I think you misunderstood my argument. The designer used a common blueprint AND mechanisms, such as non-random mutations, that implemented this blueprint. The study supports the front loaded argument that the designer used a common blueprint to create those patterns. But, I was not suggesting ihat the mechanisms used to implement the blueprint was supported by the study.
Other studies I provided do demonstrate non-random mutations though
Speak for your own model, John. I told you numerous times that the origin of life and species are both part of the common design model. It cannot be separated because it is inherent within the front loaded hypothesis.
Then, you just made my point that functional ERVâs and psuedogenes would confirm common design and therefore show that certain similar speceis are not related.
This is because both models predict nested patterns, which would require a unique prediction that separates the two models.
Humans are contingent beings. God is a human as well BUT non-contingent, which means he is immutable and perfect. He cannot violate his own nature and will because it is logically impossible.
Wrong, we have very good reasons based on this study:
"Horizontal gene transfer (HGT) enables organisms to acquire pre-existing adaptive characters from other organisms, regardless of phylogenetic distance. Thus, instead of genetic traits within lineages always emerging gradually through successive mutations and selection, evolution is accelerated as a parallel process, where inventions made in different lineages can come together in a single cell through HGT. Several cases of transfers that conferred a specific novel adaptation to the recipient lineage have been documented. "
⌠In addition to sharing metabolic capabilities between unrelated organisms, HGT also plays an important role in creating new functional roles for existing proteins by assembling new metabolic pathways. Some pathways that changed the face of planet Earth, such as acetoclastic methanogenesis in Methanosarcina [2,3] were likely assembled through gene transfer." [emphasis added]
The HGT and common blueprint the designer used is what produces those same patterns WITHOUT violating them because HGT played a huge part in developing unicellular and multicellular organisms:
"Mobile genetic elements, including transposons, plasmids, bacteriophage and self-splicing molecular parasites, have played a crucial role in facilitating the movement of genetic material between organisms [7,8]. These elements likely already played a similar role in the early stages of lifeâs evolution [9], and continue to play a role even in multicellular eukaryotes. For example, pervasive transfer of rolling-circle transposons (also called helitrons; [10]) has been reported to occur in many species of insects, plants and vertebrates, primarily through insect viruses as vectors [11]. During transposition, helitrons often capture genes or gene fragments from their host, and can therefore significantly influence the evolution of their host genome, for example through modifications of the transcriptome and in generating new genes [12]. These parasitic entities have been implicated in altering structural, functional and epigenetic variability of their host genome [13], consequently enhancing the evolvability of species and lineages. [emphsis added]
Ancient horizontal gene transfer and the last common ancestors | BMC Ecology and Evolution | Full Text (biomedcentral.com)
. HOWEVER, non random mutations, such as cytosine deanimation would still produce convergence or basic types without violating nested patterns.
No, you just misunderstood the context of what we were discussing.
I was using the laws of logic to determine this NOT the laws of nature. Humans are contingent beings. God is a human as well BUT non-contingent, which means he is immutable and perfect. He cannot violate his own nature and will because it is logically impossible.
Who said anything about the laws of nature? Red herrings all the way.
In addition, explain how the âlaws of logicâ led you to know that God âcannot create and develop a world that does not have God intimately involved in the process every step of the way because it would conflict with his âPersonalâ natureâ, considering a Deist God can do exactly that too?
It is not. Viruses do not develop into unicellular, complete organisms. Viruses in fact cannot reproduce except by hijacking the replication and protein-making mechanisms of a complete cell. Were viruses once very different from modern viruses? But if they were that different, they would be cells, not viruses.
Further what does âre-used microbial partsâ mean? What does âdevelop basic typesâ mean? Are we talking about common descent, fiat creation, or Frankenstein here? Cytosine deamination is not a magic word that poofs new organisms into existence. Itâs one type of mutation; itâs the single most common one but it also doesnât do much, and genomes differ from each other by much, much more than just C-T transitions. This is all nonsense.
Question: do basic types descend from other basic types or donât they? If they donât, what cause the nested hierarchy among types? If horses, for example, are a basic type, why do they group with rhinos and tapirs to the exclusion of other herbivores? Why do fossil rhinos and tapirs look more and more similar to fossil horses as we go back in time?
Your theory is more incoherent than ever.
Nonsense. HGT disrupts nested hierarchies. Your sole reference shows that any semblance of nested hierarchy from HGT results when HGT is more common between close relatives than distant relatives. But âcloseâ and âdistantâ only make sense if there is a tree of common descent on which the HGT is superimposed. Otherwise we would expect no nested hierarchy from HGT, and certainly not the same nested hierarchy in different parts of the genome.
âCommon blueprintâ is meaningless and could demonstrate any pattern you liked or no pattern at all. There is no reason to expect a nested hierarchy from it. Any mechanism used to instantiate this blueprint is so far wholly opaque.
Again, nothing you cite ever means what you imagine it does. The octopus reference is a particularly egregious example, but everything else is similar.
The hypothesis is so far so confused and muddy as to communicate nothing.
No, I didnât. You canât read even one simple sentence.
Merely repeating the same vacuous sentences over and over doesnât make an argument for you.
That means nothing. âCommon blueprintâ means nothing. HGT does not create nested hierarchy unless there is an underlying phylogenetic tree. And again, none of your references supports the claim you use it for, not even if you bold random bits.
Itâs hard to know whether to laugh or be sad for you. Both?
We have basis to say that RNA viruses were developed within the pool of self-replicating RNA sequences because RNA viruses have not yet been observed in nature or laboratory to self-replicate without the help of an intelligent designer.
Poliovirus Baked From Scratch | Science | AAAS
More importantly, they display elements of functionality, and perform important purposes in ecosystems that could only be done by an intelligent designer according to PACE experiments:
Both experiments combined show how God created and designed viruses to function like the viruses we see in the deep-sea oceans I mentioned, such as theseâŚ
Major viral impact on the functioning of benthic deep-sea ecosystems | Nature
Viruses manipulate the marine environment | Nature
Before the leftover meteorites, which contain amino acids, were clumped together to form the primitive earth 3.8 billion years ago after the late bombardment event, virus-like RNA molecules were created within the deep-sea hypothermal vents of the earth.[1] Then, these virus-like RNA molecules evolved into different species of unicellular organisms where they would undergo a heavy amount of HGT from those same viruses created within the deep-sea oceans.[2]
For instance, the mineral surfaces of the earth would have contributed centrally to the linked pre-biotic problems of containment and organization by promoting the transition from RNA virus particles that lack important proteins to highly ordered local domains of key bio-molecules of a DNA virus or molecule [3].
Furthermore, viruses in the deep-sea oceanic vents , where the viral production in these deep-sea benthic ecosystems worldwide, is extremely high. In fact, we find that RNA viruses represent the most abundant form of organisms within the worldâs oceans compared to any other micro-organism and cover every ecological niche around the globe [4]
[1] A 3,800-million-year isotopic record of life from carbon in sedimentary rocks | Nature
[2] Hot crenarchaeal viruses reveal deep evolutionary connections - PubMed (nih.gov)
[3] Mineral Surfaces, Geochemical Complexities, and the Origins of Life (cshlp.org)
[4] Major viral impact on the functioning of benthic deep-sea ecosystems | Nature
[quote=âJohn_Harshman, post:347, topic:15208â]
Further what does âre-used microbial partsâ mean? [/quote]
This is what I meanâŚ
As I referenced before, scientists were able to synthesize the RNA molecules of a virus and reconstruct a virus particle from scratch. They accomplished this by creating another virus and used itâs parts, such as specialized proteins (enzymes), to construct an RNA virus to solve the problem of an unstable RNA.
This is how human designers operate all the time. They use preexisting mechanisms, material parts and digital information to assemble designs in order to achieve a purpose.
I am saying God formed basic types within the primitive earth like a clay potter once he developed the microbial parts that I just mentioned. So I guess âFrankensteinâ design is the best way to describe it as you mentioned because cytosine deanimation is all about unpacking buried design wovened within the genetic code.
According to cellular automata, a complete self-replicating automaton must consist of three components: an UC, a (instructional) blueprint and a supervisory unit. These functional components are required to produce successive generations of artificial life, which happens to produce patterns that look like nested hierarchy.
[Tree (automata theory) - Wikipedia](Tree (automata theory) - Wikipedia
Moreover, the universal common designer, the common blueprint, and HGT/ non-random mutations would be the biological version of Von Neumanâs Universal constructor, blueprint, and supervisory unit
For exampleâŚ
âThe [Universal Constructor] forms the foundation of von Neumannâs theory on self-replicating automata. However, an UC is a mindless robot, and must be told very specifically exactly what to do in order build the correct object(s). It must therefore be programmed to construct specific things, and if it is to replicate then it must also be provided with a blueprint of itself.ââŚ
"âŚvon Neumann proposed that in the biological case the blueprint must play a dual role: it should not only contain instructions such as an algorithm, to make a certain kind of machine (e.g. the UC) but should also be blindly copied as a mere physical structure, without reference to the instructions its contains, and thus reference itself only indirectly.
This dual hardware/software role mirrors precisely that played by DNA, where genes act both passively as physical structures to be copied, and are actively read-out as a source of algorithmic instructions. To implement this dualistic role, von Neumann appended a âsupervisory unitâ to his automata whose task is to supervise which of these two roles the blueprint must play at a given time, thereby ensuring that the blueprint is treated both as an algorithm to be read-out and as a structure to be copied, depending on the context." [emphasis added]
The algorithmic origins of life | Journal of The Royal Society Interface (royalsocietypublishing.org)
HGT and non-random mutations implement the genetic code in the same fashion and ,thus, would naturally produce those nested patterns AND similarities among separately created basic types.
Donât forget this article as well:
"Although horizontal gene transfer (HGT) is usually considered a disruptive force in recovering organismal phylogeny, it creates important phylogenetic information. In the ânet of lifeâ, the recipient of an ancient gene transfer can be the ancestor of a lineage that inherits the transferred gene; thus, the transferred gene marks the recipient and its descendants as a monophyletic group. "
This is because you are forgetting the other two functional components that contribute to producing those patterns: the genetic code and non-random mutations through cytosine deamination.
The Common blueprint I was referring to is just the genetic code that existed prior to LUCA. Again, cytosine deanimation unpacks and draws from that preexisting template like a positive feedback loopâŚ
So it is the genetic code that does all the work by accessing this mechanism.
I thought you were referring to science and empiricism when I said that.
No, a deist God would merely create designed laws at the beginning of the universe and then let it run its course. In contrast, a personal being would have an intimate relationship with it.
That isnât a response to my objection.
That makes no sense, and your references do not support the claims you make here.
And that was followed by a non-explanation of what you mean.
That means that all the basic types were formed 3.8 billion years ago?
None of this is a reply to the questions I asked you. Are you by any chance a bot?
You donât understand that this contradicts your claim. Itâs talking about actual common descent, not illusory common descent.
Neither of these contributes to any patterns. The genetic code is (with a few expections) invariant and supports no phylogeny. Cytosine deamination is just a form of mutation that occurs in common descent. It doesnât simulate common descent. It is common descent.
If so, then it doesnât produce a nested hierarchy. Or perhaps when you say âgenetic codeâ you donât actually mean the genetic code, which is the mapping between nucleic acid triplets and amino acids during translation. Again, there is no reason to expect any sort of common blueprint to produce a nested hierarchy.
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I donât know how you arrived at that âthoughtâ from my reply.
Thatâs not a response to my question. A deist God is capable of making a universe like ours, and so can an intimate or personal one, so how did the âlaws of logicâ alone allow you tell which God allegedly made the universe?
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Not this garbage again:
How could anything be created within the deep-sea vents of Earth before the earth was formed?
Thatâs completely bonkers.
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Ok, let me add more details and information to the model to clear things up:
Around 3.8 billion years, billions of viroids, which contained all the required genes to make certain evolutionary trajectories more likely, were created within the deep-sea hypothermal vents of the earth.
*Through group selection, these viroids evolved into different species of unicellular organisms, undergoing an extensive amount of HGT leading up to multicellular organisms. *
After the transition to multicellular organisms, the designer used HGT and cytosine deamination to develop them into basic types (starting with fish and ending with humans) from different times and global locations. These basic types undergoing an extensive amount of HGT would branch into diverse progeny to deliberately pioneer environments worldwide over long epochs.
Yes apparently. For instance, the Mimivirus does not differ appreciably from parasitic bacteria, such as Rickettsia prowazekii â(Raoult et al. 2004;Wessner, David R. 2010).
In fact, âBecause its lineage is very old and could have emerged prior to cellular organisms,[22][23] Mimivirus has added to the debate over the origins of life. Some genes that code for characteristics unique to Mimivirus, including those coding for the capsid, have been conserved in a variety of viruses which infect organisms from all domains. This has been used to suggest that Mimivirus is related to a type of DNA virus that emerged before cellular organisms and played a key role in the development of all life on Earth.[22] â (from Wikipedia)
Why would this be the case?
I was just referring to HGT and its further application into the development of basic types.
I was just referring to the symbiosis and cooperation process that led to the formation of multicellular eukaryotes according to science.
HGT
HGT from ERVâs is the answer because of their capacity to disrupt the endogenization process of invading retroviruses. ERVs may protect the host cellâs genome from retroviral infections through competitive inhibition, which would prevent the transmission of the invading retrovirus to other cells. For this reason, the similarity of the ERVâs to retroviruses is crucial.
Good question. I donât know right now, but It is a good research question for Telelogists who advocate for an intelligent design perspective.
The genetic code is a human language. Moreover, human languages, which have common ancestors and are derived by descent with modification, generally can be classified in objective nested hierarchies as Theobald suggested.
This means that the frequent implementation of this genetic code (with the use of HGT and non random mutations) would produce nested patterns.
According to cellular automata theory, we do.
A personal God creates AND develops the universe into existence while a deist God merely creates it.
And I do not use the laws of logic alone to argue why God would not be inconsistent. I also based it on empirical evidence.
That doesnât clear things up at all. What you describe here is common descent, which you previously denied. One must conclude that you have no real idea of the meanings of the sentences you spout, many of which may not in fact be your own. Your attempt to clarify has resulted in even greater confusion.
What you say next doesnât support that claim. The Wikipedia article you quote (without a clear citation) misunderstands its primary source, which you should have looked up.
A virus capable of replicating its own DNA, transcribing its own RNA, translating its own RNA into protein, and metabolizing to gain the energy for all that fits the definition of cellular life. Viruses donât do those things.
In that case, basic types are descended from other basic types, and you are now arguing for common descent. And the nested hierarchy among basic types, according to this hypothesis, is explained by common descent. You have switched from a theory of separate creation to a theory of theistic evolution.
The question was why horses group with rhinos and tapirs to the exclusion of other herbivores. You response has nothing to do with that.
It is not. If itâs a language, itâs a language with only 64 words. And itâs not human.
Human languages, interestingly, show objective nested hierarchy precisely because they are related by common descent. You contradict yourself constantly. Nor does that have anything to do with the genetic code, which does not produce nested patterns, being nearly invariant.
You only think so because you donât at all understand your sources. So, above, you both confirm and deny common descent. You answer questions with irrelevant, canned responses. Why should anyone continue to talk to you?
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A deist God can create a fully developed universe and not interfere with it afterwards, but allow to run itself via designed natural laws. That takes you back to square one. How did you discover, with logic alone, that the creator is a personal one and not deist?
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RIght, but this is why my model cannot be a description of common descent. In my model, viroids were created by divine fiat or top-down causation. In other words, they did not self-replicate and there were more than one group of viroids that turned into unicellular organisms.
Moreover, virsuses are not considered part of the universal tree of life .
I am very confused by this John. How are you defining separate creation or progressive creationism? And how can I be arguing for universal common descent when I specifically saidâŚ
the designer used HGT and cytosine deamination to develop them into basic types (starting with fish and ending with humans) from different times and global locations.
In other words, each basic type descended from multicellular organisms but NOT other basic types.
Also, how do you know HGT can only create or mimic nested patterns unless common descent exist already?
The biased gene study claims it maintains AND creates the same patterns:
âThe more genes that two lineages transfer between each other, the more similar that the lineages become and the more frequently that they will continue to exchange genes [16]. If genes are mainly transferred between close kin, then gene transfer reinforces similarity, regardless if it is because of shared ancestry or biased HGTâ" [emphasis added]
Again, HGT creates the same nested patterns of vertical inheritance. So I did address it, but from a common design perspective. The shared ERV"S are common design elements employed by the Creator, not shared evolutionary history.
Thus, horses group with rhinos and tapirs to the exclusion of other herbivores because God used the same mechanism for them. More importantly, Godâs purpose in using the same mechanism to create similarity was to protect them from the transmission of the invading retrovirus to other cells:
âAs a result of biased transfer, we expect to observe similar distribution patterns between a specific gene tree and the ribosomal tree. While biased HGT can give rise to phylogenetic patterns similar to those created through shared ancestry, both processes occur simultaneously in nature. Through biased transfers, a group then may be defined by the multiple transfers of the same gene among different closely related taxa, generating cohesion among the recipient organisms in terms of genetic similarity.â
Biased gene transfer and its implications for the concept of lineage - PMC (nih.gov)
Now, I know you and someone else claimed thatâŚ
" Your sole reference shows that any semblance of nested hierarchy from HGT results when HGT is more common between close relatives than distant relatives."
But, you guys never explained why this refutes my point or model since the Common Design theory accepts common descent but rejects Universal common descent.
Guess again:
"Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the non-repetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. " [emphasis added]
Prove it then. HOW? I think it is definitely the other away around here.
So let me start from scratch with the definition of God where I will exclude some attributes at the start to break it down for you and show why your objection is invalid. God is an omnipotent/ omnipresent/ omniscient /eternal /necessary/ spaceless timeless immaterial cause (i.e. a mind) who is the creator and sustainer of our Universe⌠Believe it or not, many physicists essentially believe in this impersonal Spinoza/deistic force in the form of a quantum computer called the universal wave-function.
Before I add in the attribute of being Personal, letâs define it again (WIKI):
"A person is a being, such as a human, that has certain capacities or attributes such as reason, morality, consciousness or self-consciousness, and being a part of a culturally established form of social relations such as kinship, ownership of property, or legal responsibility.
Now, if this spiritual force is still considered an existing entity when we include the attribute of personhood, what would we expect from it?
We would expect it to establish a relationship with another person based upon this definition. I am sure you would agree that this additional attribute would explain why we exist, but it would not explain why God exists.
For instance, since being a person involves being with other persons, it would imply that he needed to create us in order to be who he is. As a result, it would contradict the self-existing attribute of necessity he possesses. In order to be consistent with the law of identity, we have to incorporate the Trinity concept and suggest there were other pre-existing persons that existed eternally together as one being like a three-headed dragon.
However, although this new concept would explain his existence, it would no longer explain why we exist since he does not need us to exist to be complete. This is where the attribute of omnibenevolence comes into play so letâs define it first:
All-just , all-loving, and all-good/morally perfect
God the father (i.e. Yahweh) represents the all justness
God the son (i.e. Jesus) represents the all-loving.
God the holy spirit represents the all-goodness/moral perfection
With the inclusion of the omnibenelovence attribute, it explains why Godâs love is not limited only to the Trinity or humans and thus explains our existence, hence John 1:1-3 and even John 3:16 in its reference to Jesus.
To sum up, all the other attributes besides personal and omnibenevolence represent the Godhead, which is a mind or spiritual force. The three persons represent the personhood and omnibenevolence.
Without these attributes, we would not even exist in the first place since God obviously does not need us to exist but just wants us to exist to bring as many people as he can in a loving relationship with him.
This is why the point you made is invalid because the intrinsic desire to have a meaningful relationship with life needs to exist in all possible worlds or else you would not even be able to ask the question in the first place.
A deist God has all of these attributes.
Which is irrelevant to my question.
You wanted to define personal, but ended up defining person. You are really confused.
You obviously donât understand what deism is all about. A deist God is a person too!
This is what you expect for a personal God, not a deist one.
No, it doesnât. A deist God can create us and not interfere in our affairs. A personal one would create us and want to be very much part of our lives.
A deist God doesnât need to.
God doesnât need us to be who he is. This thinking results from your lack of understanding of what deism is.
All of this is irrelevant to deist God who can make the universe and let it run itself based on provided laws.
For the love of God, a deist God doesnât need the attributes you mentioned to create humans. He could just make us and let us be.
I asked you a question and a valid one too. Donât tell me you canât distinguish between a question and an argument?
You have written absolutely nothing to show how logic alone tells you our universe was made by a personal God and not a deist one. I am not surprised as most of your comments in this thread and previous ones have been mostly vacuous.
I am sorry for wasting my time. I am done.
How would viruses do any of that if theyâre unable to replicate? Your model makes no sense. Why not just posit the direct creation of unicellular organisms?
Thatâs an understatement.
Thatâs a description of common descent. Again, HGT and cytosine deamination are processes that do not operate except in a context of descent.
Gibberish. What multicellular organisms do not themselves belong to some basic type? And descent from other organisms is common descent.
Thatâs what your sole reference for this says. HGT mimics common descent when it occurs between close relatives. What do you think âclose relativesâ are?
But it doesnât. It actually violates those patterns. That in fact is how we detect it.
Then why do both the insertions and sequences of the ERVs show a nested hierarchy? Why do they fit into the same nested hierarchy for different ERVs?
Simple enough: whatever common descent you accept, nested hierarchy extends far beyond that. So your model (which you still havenât managed to articulate) is incompatible with the data.
That isnât talking about the genetic code as the term is actually used in biology. When you use your personal definitions for words, is it any wonder people donât understand you? But notice, again, that your analogy to human languages in order to refute common descent doesnât work, since human languages are in fact related by common descent.
Letâs recall that you tried to refute a claim about octopus retinas by citing a sentence that talked about crustacean eyes being a target for attack. Thatâs only the most glaring misreading. You consistently choose references that have a few words you like, but you donât pay attention to how those words are arranged to make actual statements.
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The mineral surfaces of the hyperthermal vents would have contributed centrally to the linked pre-biotic problems of containment and organization by promoting the transition from RNA virus particles that lack important proteins to highly ordered local domains of key bio-molecules of a DNA virus or molecule.
This would explain why viruses in the deep-sea oceanic vents , where the viral production in these deep-sea benthic ecosystems worldwide, is extremely high. In fact, we find that RNA viruses represent the most abundant form of organisms within the worldâs oceans compared to any other micro-organism and cover every ecological niche around the globe.
Because it would not be consistent with observations:
"HGT depends upon the universality of the genetic code. Every known organism uses the same twenty amino acids (the infrequent usage of an additional two, selenocysteine and pyrrolysine, notwithstanding), and with few exceptions these are decoded by tRNA in the same way. Without a universal set of amino acids and decoding system, genes transferred between organisms could not be translated and expressed as proteins, and lineages would be isolated by their own distinct âgenetic dialectâ.
âŚThe presence of HGT early in the evolution of life before the time of LUCA is also supported by the optimality of the genetic code itself, which likely depended upon extensive HGT to become established [30]."
What do you mean by that? Are you saying those mechanisms could only have been used to develop basic types into another basic type, but NOT from multicellular organisms to basic types for animals?
To me, multicellur organisms are just parts God used to form basic types like a clay potter uses clumps of mud or sand to build castles or pots. But, if you still view that as common descent, then thatâs fine. I think this is inaccurate though because it does not involve the evolution of sex, cell differiriation and consciousness, which is consider the transition from a basic type to another basic type.
Yes, but it is NOT the only thing it says. The article said that close relatives are family and genus, which happens to be the same level of a basic type. So I donât get your point here, especieally if you view the process leading up to basic types as common decent.
Not according to the study:
âGene transfer is often viewed as creating conflicting relationships in microbial phylogeny, resulting to topological discrepancy between the gene trees and the species tree or organismal tree [15]. In the case of horizontal acquisitions from distant relatives, the gene of the recipient taxon would exhibit high similarity to the donor group, despite the evolutionary distance that separates them. On the other hand, when closely related partners in a group exhibit preferences for exchanging genes with one another, such sharing may eventually lead to cohesion of the group [16].â [emphasis added]
HGT among ERV"s, which can happen.
Because ERVâs have other functions for them, such as the innate immunity of the early-stage embryo:
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells | Nature
Well first off, the article never said that the creation of those patterns from HGT could not or does not happen beyond the family level. It just said it was less common. Secondly, if you view the process leading up to basic types as common decent, then the model is still consistent with the data.
Third,the genetic code is also a mechanism that would produce those patterns, which leads me to address your objectionâŚ
Right, it does not. But, you are making my point. Here is the article explaining why:
âNearly at the same time, the above mentioned hallmark assumptions in molecular biology and genetics were falsified through empirical evidence in the roles of non-coding RNAs and viruses in evolution and development of all domains of life. At the current stage, the dominant role of RNA biology and the dramatic comeback of virology changes our picture of the genetic code.â
No, the real issue is that you seem to be incapable of separating the concept of common descent from nested hierarchy. They are not synonymous. You keep imposing common descent onto those patterns. The common blueprint/language the designer used is what produces those same nested patterns in language WITHOUT violating them.
You provide irrelevant âresponsesâ to both questions. And it appears that both responses quote without attribution from someone else.
Iâm saying that multicellular organisms would be basic types that in your theory as expressed evolve into other basic types. If that isnât what you meant to say, what did you mean to say?
I have no idea what you think you mean.
If HGT happens between relatives to mimic common descent, it only mimics common descent in taxa that are in fact related by common descent. That canât explain nested hierarchy above the level of genus and family. And thus you canât explain why, for example, mammals show nested hierarchy between families and orders, or why there is nested hierarchy between mammals and other vertebrates, etc.
Bold text for things you donât understand doesnât change it into what you imagine it to be.
What do you mean by that?
Again, not a response to the question I asked. You still resemble a bot that searches for key words without any regard to the sentences they appear in.
I grow tired of the meaningless replies.
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I donât understand what you are asking then. Again, the origin of life model I presented is consistent with observations and the RNA world hypothesis:
âDiener initially hypothesized in 1989 that viroids may represent âliving relicsâ from the widely assumed, ancient, and non-cellular RNA world, and others have followed this conjecture.[12][13] Following the discovery of retrozymes, it is now thought that viroids and other viroid-like elements may derive from this newly found class of retrotransposon.[14][15][16]â
Yeah, this is what I meant as long as you were not referring to complex multicellular organisms. For instance, the common descent model claims "Multicellularity has evolved independently at least 25 times in eukaryotes,[7][8]
"âŚHowever, complex multicellular organisms evolved only in six eukaryotic groups: animals, symbiomycotan fungi, brown algae, red algae, green algae, and land plants. "
To be clear, my model does not view primitive multicellular organisms to be basic types before the six complex groups were created. Again, they are just parts God used to form those groups like a clay potter uses clumps of mud or sand to build castles or pots.
Moreover, the primitive multicellular organisms independently evolved into other major animal groups, such as fish, amphibians, reptiles, etc.
This is probably irrelevant to point out, but I just want to make sure we are on the same page.
So you are telling me that even thoughâŚThe article never said that the creation of those patterns from HGT could not or does not happen beyond the family level. This means there still could be a certain amount of HGT that was responsible for the patterns. Secondly, My model allows for common descent above the class level.
Despite these reasons, you are saying HGT would still not fully explain nested hierarchies from a common design model?
If so, then I definitely think the genetic code and micro-tubules can explain the rest.
I am saying that the nested relationship between ERVâs came from HGT as well, which created those patterns. I was compelled to say this because of what I read on here:
â. There are no ancestral viral lineages
No single gene has been identified that is shared by all viruses. There are common protein motifs in viral capsids, but these have likely come about through convergent evolution or horizontal gene transfer.â
Then, I donât understand the question then or the point of it.
Yes, and thatâs probably because you donât actually read, just scan for key words. At this point, Iâm suspecting that nothing can be done.
That clarifies nothing. What, in your own words, do you think all that signifies?
Thatâs not in any way clear.
Nor is that. It certainly sounds as if you have basic types evolving from other basic types, and yet you have denied that repeatedly. We have to go back to basics: what is a basic type? How are basic types related to each other? Are fish a basic type or are there multiple basic types of fish? If the latter, how are different basic types of fish related to each other, if at all?
This is hopeless.
We are not. You donât seem to be on a page at all, just on top of a pile of words scattered at random over the floor.
There is no common design model, and you have given no reason why HGT should be organized into a nested hierarchy.
Unable to determine what that sentence is supposed to be about.
What follows has nothing to do with what preceded it.
Again, you seem not to understand anything, either what anyone else says or what you quote or what you say yourself. I canât see a solution to that problem.
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