Then, tell me why the Competitive Endogenous Hypothesis does not explain why pseudogenes show a nested hierarchy in both location and sequence. How come you disagree with RTB?
BTW, I am not sure how you would know about my model better than me.
Then, explain why you think functional psuedogenes would still count as evidence for common descent. Why do you disagree with the guy in the article who argued that they are not expected from the common descent model?
Because it simply doesnât follow that they should exhibit a nested hierarchy at all, much less why itâs generally speaking the same phylogeny you get from other genomic loci, or other forms of data.
Because they show a nested hierarchy regardless of whether they are functional or not.
What article, and what argument does he make?
So this explanation from RTB does not explain it?
âDuplicated pseudogenes not only exert a sponge effect but also serve as decoys that allow the transcripts of the intact genes to escape degradation and to be translated into proteins.â
NO, I am asking why we would expect there to be function in those instances because that is what @John_Harshman is suggesting apparently.
From the article:
"All of the examples of functionless sequences shared between humans and chimpanzees reinforce the argument for evolution that would be compelling even if only one example were known. This argument can be understood by analogy with the legal cases discussed earlier in which shared errors were recognized as proof of copying.
The appearance of the same âerrorââthat is, the same useless pseudogene or Alu sequence or endogenous retrovirus at the same position in human and ape DNAâcannot logically be explained by independent origins of the two sequences. The creationist argument discussed earlierâthat similarities in DNA sequence simply reflect the creatorâs plans for similar protein function in similar speciesâdoes not apply to sequences that do not have any function for the organism that harbors them.
The possibility of identical genetic accidents creating the same two pseudogene or Alu or endogenous retrovirus independently in two different species by chance is so unlikely that it can be dismissed. As in the copyright cases discussed earlier, such shared âerrorsâ indicate that copying of some sort must have occurred.
Since there is no known mechanism by which sequences from modern apes could be copied into the same position of human DNA or vice versa, the existence of shared pseudogenes or retroposons leads to the logical conclusion that both the human and ape sequences were copied from ancestral sequences that must have arisen in a common ancestor of humans and apes."
No, you explain why pseudogenes show a nested hierarchy. You can use the Competitive Endongenous Hypothesis if you like, but you have to actually explain why it predicts a nested hierarchy. For extra points, explain why this hierarchy is the same one shown by other data.
Because they show a nested hierarchy, both within the taxa that have a pseudogene and acros taxa that have the original gene.
Are you sure he did? I havenât seen any such claim so far. Better check again.
No, it doesnât. If you think it does, you need to explain your reasoning.
For the record, Iâm suggesting no such thing. You canât seem to understand any of your sources.
You misunderstand again. That article merely says that shared mistakes are evidence. It doesnât say that shared functional sequence are not evidence.
I was actually using it to explain why shared psuedogenes do not demand a common descent interpretation but would be better explained by common design.
(Limited) common descent better explains nested hierarchy.
You specifically saidâŚâeven if pseudogenes are functional, theyâre still evidence of common descent.â
This contradicts what the article suggestedâŚ
"The creationist argument discussed earlierâthat similarities in DNA sequence simply reflect the creatorâs plans for similar protein function in similar speciesâdoes not apply to sequences that do not have any function for the organism that harbors them.
The possibility of identical genetic accidents creating the same two pseudogene or Alu or endogenous retrovirus independently in two different species by chance is so unlikely that it can be dismissed.
Since there is no known mechanism by which sequences from modern apes could be copied into the same position of human DNA or vice versa, the existence of shared pseudogenes or retroposons leads to the logical conclusion that both the human and ape sequences were copied from ancestral sequences that must have arisen in a common ancestor of humans and apes."
If you want to make sense of that âexplanationâ, you have to deal with nested hierarchy. Just giving pseudogenes a function doesnât distinguish between separate creation and common descent. âCommon designâ, of course, has no real meaning.
But that limited common descent extends to all the taxa with the pseudogenes youâre talking about, so the pseudogenes werenât separately created.
No, it doesnât. Not even the bit you bolded. You have to stop just quoting and make some actual argument.
Do you know what a nested hierarchy is because this doesnât make any sense?
Correct. That does not explain why there should be a consistent nested hierarcy. You will notice that no explanation is provided, all it does is provide a rationalization for why there should be a pseudogene-sequence that doesnât code for a functional protein, that is similar to a corresponding protein coding gene that still works as a protein coding gene. It does not explain why sequences of shared similar pseudogenes between species should exhibit a consistent nested hierarchy.
No, youâve misunderstood. Both functional and nonfunctional gene-sequences are evidence for common descent because they exhibit a consistent nested hierarchy.
Creationists respond to the nested hierarchy by declaring (ineffectively) something like âsimilar organisms = similar genesâ, mistakenly thinking this explains why there should be a consistent nested hierarchy in the sequences of shared similar genes.
Now, disregarding for a moment that this explanation doesnât work, biologists respond that there being non-functional pseudogenes just makes it all the more difficult for creationists to explain why these too should exhibit a nested hierarchy, as given that these pseudogenes really are nonfunctional, the creationist rationalization that more similar organismal physiology should constrain genes to also exhibit more similar gene sequences stops working, as the constraint posited to explain the similarity is absent(no function = no functional constraint on sequence to match a particular phylogeny).
Creationists like you then respond that there is evidence that SOME pseudogenes are functional, providing a putative rebuttal to the argument from pseudogenes. Itâs just that thereâs two problems with this.
First is that the rationalization is wrong. There is simply no good evidence that physiologically more similar organisms SHOULD require more similar gene sequences(it might make intuitive sense that such a constraint should exist, but in fact it doesnât biochemically work, as there are innumerable numbers of entirely different gene-sequences that can do the same job, and conversely completely identical sequences can too of course, thus eroding any explanation for why there should be nested clade patterns in the sequences). And second, the creationist rationalization from there being some functional pseudogenes effectively constitutes a hasty generalization fallacy. Having found a small handful of examples of functional pseudogenes does not support an extrapolation to the many thousands of other pseudogenes.
Iâm sorry but I canât make sense of what you were trying to argue here, now. In the context of @John_Harshmanâs replies to you, the part of your post I responded to bears no connection to the talk.origins article you quote. Iâm going to need some more clarification on what youâve been trying to argue.
I want to first thank you for giving me a detailed response because it was starting to lack more and more from Johnâs responses. Now, it does not look like you have been following our conversation closely because we were discussing instances of nested hierarchies on a smaller scale rather than universal. I have actually explained already why we would expect to see consistent nested hierarchies from a common design perspective.
As I told him, God just re-used the same mechanism in the form of HGT to create biochemical similarities among all living things that naturally gives the appearance of common ancestry because HGT mimics the same process:
Biased gene transfer mimics patterns created through shared ancestry | PNAS
@John_Harshman responded withâŚ
I responded to him by mentioning that we would expect to find at least some instances of common ancestry because the common design model allows for the evolution of de nova created organisms that evolved afterwards into kinds.
At this point, John started to make a different point than he made previously and suggested that I still need a hypothesis that distinguishes both models, which leads me to address the next thing you saidâŚ
Your last response ended up actually making the same objection. But, my point was that functionless pseudogenes is expected from a common descent model. On the other hand, the common design model would expect to see function from them since it uses a known mechanism that could create those shared features without demanding a common descent interpretation.
This was the crux of the argument from the guy in the article. He argued that common descent was the only explanation for the data because there was no known mechanism that could produce the same effect. The study I provided shows that this is false.
Now ,as far as WHY god would design shared sequences, I told you and John already. The competitive endogenous virus hypothesis provides an adequate explanation as to why.
True, but it also does not mean we wonât find function in the future for the majority of them.
So let me get this straight. You think God created an organism, then took genes from that organism and used them to create another, then mutated both.
Then took the genes from both, put them into four more, then further mutated the four new and the two old ones.
Then took the genes from all four new(now old), put them into eight more new organism, then mutated the eight new and the six(4+2) old again.
Then did the same for about 16 new, further mutating these along with the 14(8+4+2) old ones.
Something along those lines, for millions upon millions of species - basically faking the evidence for common ancestry by aping the process - by using branching lines of âhorizontalâ descent with modification?
And God of course makes sure to once in a while make some of his fake lineages go extinct, leaving some of his progressively and increasingly more and more derived creations with fewer close relatives than others, some with no close relatives, and some with huge numbers of very recent relatives. As if extinction has really happened a lot on some of his fake branches. He must have really got tired of all the trilobite copy-pasting-with-new-mutations. âEnough with the new compound eye structures, you guys are fucked. BE GONE!â - He said, and saw that it was good.
So itâs progressive creation with copy-and-paste of genes(sprinkled with new mutations) from previous creations, but with God also going back and further mutating old creations so these too look like they further diverged from the âbranch pointâ. Thatâs fantastic! Itâs almost like God is doing his very best to make it look like evolution really happened. Now we just need God to do a fake chronological order in the fossil record, creating single-celled organisms first, and then to wait about 2 billion years before creating a eukaryote. Then at various million-year intervals, create new derived organisms from previous creations, making sure to further fake-evolve both. Then to match the creation order with various geological and climactic changes in the planetâs history. No use for penguins(âhorizontallyâ derived swimming birds⌠lol, good one God) and polar bears in the Cryogenian I suppose.
And to top it all off, God also made absolutely sure to make life intrinsically capable of actually evolving along actual branching lines of genealogical descent.
I tried.
Thatâs an interesting paper but some of the claims you are making do not derive from it.
First, multicellular eukaryotes like mammals, reptiles, fish, birds, insects etcetera do not engage in HGT with each other, so right off the bat your claim that HGT accounts for all the patterns of common descent between all extant organisms is dead wrong.
Second, this horizontal gene transfer that is biased by vertical inheritance seems to be restricted to âlower taxonomic levelsâ. You probably missed this part from the paper:
So, as per this paper, even in prokaryotes where HGT is common, it does not account for all observed patterns of common descent.
In addition, you have to realize that its vertical inheritance which creates the patterns of shared ancestry, while biased HGT âmaintainsâ it. Several factors can make HGT muddle phylogenies, but it appears there are factors that could make it not obfuscate and even reinforce phylogenetic signals. You probably missed these parts of the paper:
The signal of vertical inheritance is still present in the data, but HGT must be accounted for to accurately understand the evolution of prokaryotes.
This is a baseless claim from you, not supported by even the paper you cited. The patterns of common ancestry pervade the data, while those we would expect to find for separate origins sorely lacking. Donât forget I shared a paper that sampled genomes across many taxonomic groups to test common ancestry versus separate origin events, and common ancestry beat it hands down.
We expect both functionless and functional genomic elements to be inherited by descendant populations from an ancestral population under common descent and thatâs what see.
LOL. I assume this âknown mechanismâ is HGT but you have a wrong perception of the process. HGT happens to both functional and functionless genetic elements. In fact, a large fraction of horizontally transferred material tends to be neutral (they provide no benefit to the recipient). This form of HGT you speak of, which happens for only functional elements is fictional.
As I showed above, vertical inheritance creates the patterns of common descent, but biased HGT can maintain those patterns among closely related prokaryotic species.
You have being assuming all along that God used HGT to transfer genes between species to create a façade of common descent. I would like to know how you know this?
The study you cited shot you in the leg.
Again, when I said that God re-used the same mechanism to create molecular similarities, I was mainly referring to the de novo created organisms. In other words, I would say half of it is vertical heritance and the other half is HGT. But, we have to find out from future observations and experiments to be more precise about the extent in which HGT occurred.
Well, there is another reason why God would create those similarities that I did not tell you.
HGT is supposed to be the mechanism used by God to create biochemical similarities among de novo created organisms in order to protect advanced life from incoming harmful viruses.
For instance, as Hugh Ross suggested, "the structural and functional features of the preexisting ERVs (i.e., their capacity to copy themselves and move throughout genomes) are precisely what make these ERV sequences so useful. Their capacity for retrotranspositioning affords these sequences the means to disrupt the endogenization process of invading retroviruses. In other words, for the ERV sequences to operate as antiretroviral elements, they must resemble endogenized retroviruses.â
Thus, this explanation and the competitive endogenous virus hypothesis both provide adequate accounts for WHY we see shared features among living things according to the common design model.
This means that there is nothing ad hoc or post hoc about my model as you were suggesting when you were being comical with your last response.
âad hoc: created or done for a particular purpose as necessary.â
Adding things that werenât previously mentioned is literally what âad hocâ means.
What? A de novo created organism has no ancestry, so what is it supposed to have vertically inherited, when you think it is âhorizontallyâ acquiring itâs genes from other de novo created organisms?
Vertical inheritance implies a normal process of birth from previous generations of ancestors. But if an organism is being created de novo, that is without ancestors, it canât be a product of a mix of vertical and horizontal descent. Youâve completely stopped making sense.
I never said that.
As I told @Rumraket, I would say half of it is vertical heritance and the other half is HGT. But, we have to find out from future observations and experiments the extent in which HGT occurred to be more precise.
Well, this study shows itâs much more than that:
And my paper shows that pervasive or universal patterns of common ancestry is primarily an illusion because HGT mimics the same patterns:
âWe conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.â
I have already provided experiments that support this claim on other topics. Do you want me to repeat myself?
Yes, we would but I think this would primarily be a rare occurrence under the common descent model while my model suggests it would be widespread.
Why not?
Because words have meanings, and yours seem to be private. You use a term like de novo creation, vertical and horizontal descent. The way you use them make no sense to me.
A de novo created organism doesnât have vertical ancestry. Can we agree on that?
Yes, my mistake. I meant de novo created organisms for advanced life NOT simple life. Let me state the hypothesis again to be more clear:
A Universal common designer re-used a DNA blueprint, RNA viruses, and chemical constituents to separately construct animals from different locations around the globe.
These basic types of animals would NOT be static but dynamic. They would be able to adapt to changing environments and diversify into kinds over long epochs of time. This would involve the designer employing many familiar mechanisms ,such as gene drift, and a common set of solutions to address a common set of problems facing unrelated organisms in their quest for survival.
You have admitted to many such mistakes throughout your threads. That makes it look as if you are making it up as you go along.
But why?
You could have a masterful grand God that creates an evolutionary system so that the biosphere will be self-sustaining. But, instead, you insist on a tinkerer God who make mistake and has to do more tinkering to fix those mistakes.
It makes no sense.
It seems that you want to pretend that your holy book is scientifically accurate, instead of recognizing that it is a book of cultural traditions.