I have lost track of all the flip flops, changing positions, and self contradictions.
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I was thinking more of a drinking game.
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Alcoholism here I comeâŚ
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Then you need some palm wine to go along with you.
Actually, that was not the source I was referring to. I was talking about the source below it featuring Donald Prothero where he reviews the literature on state of the fossil record. It was much easier to use a secondary source since they were too many articles for me to read and list on this forum.
Very bad form to quote a quote. That makes it easy to turn it into a quote mine.
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I think he is trying to say that under a separate creation model that about 50% of DNA would fit the tree and the rest would be homoplasy (doesnât fit the tree).
Thatâs a testable hypothesis of course, but I donât think he knows itâs been tested or how to test it for himself.
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So heâs using âHGTâ just to mean âanything that doesnât fit the treeâ?
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Oh, I think I know what you are getting at now. I discussed this with @John_Harshman previously on another topic.
According to the common design model, Yes we should expect to find more examples of sequence or functional convergence between closely related organisms, which would show them to be unrelated. Here is one example of this:
Thatâs not what this study suggests:
Phylogenomic conflict coincides with rapid morphological innovation | PNAS
I know based on the mechanisms this designer uses , such as the observations of viruses and their ability to perform HGT.
Yes but only for (limited) common ancestry and if you are going to say otherwise, then you need to provide studies supporting your contentions like I have.
Major Gaps between major species in the fossil record that you acknowledged existed is the evidence showing that God did not use universal common descent.
As I told you before, God used HGT to create basic types of organisms (or original kinds) with the highest amount of biochemical similarities. Then, allowed those basic types to diverge into different kinds where those kinds became increasingly dissimilar and ,thus, it would explain the results of the study you gave me showing an increase of similarity between organisms as you go back in time.
So it is no surprise that they did not engage in HGT recently since they were de novo created with those similarities already planted in them rather than after they were constructed.
That quote you mentioned was only talking about how the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer.This is a different subject and point that they made in their paper.
This is why the bottom of their abstract said, 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
Do you see now that these are two separate things in their paper? They are not interchangeable subjects. For instanceâŚ
âFor each type of TyrRS, the observed phylogenetic pattern is created through a combination of vertical inheritance and biased HGT. It is reasonable that similar patterns of gene transfer are followed in other gene families as well (14, 15). Consequently, the degree of relatedness, as measured by the average phylogenetic signal retained in the genomes, is a function of two processes: the frequency by which organisms swap genes with each other and how long ago they evolved from a common organismal ancestor.â
After this part, they switched to the latter topic that involves the difficulty of distinguishing common descent patterns from HGT. The quote you referenced deals with that NOT the other point about HGT mimicking the same patterns as common descent.
Therefore, I found nothing within their paper that implied what you are trying to suggest. You will need to provide a different quote to support your claim about the nature of their argument.
Even if I granted this, it would not mean separate creation could not have happened because common descent does not have an origin of life model. LUCA is not the first life.
So you are making a moot point in regards to my model, which actually has a model for the origin of life.
This seems to conflict with what they said later on:
âBoth HGT and vertical inheritance are natural processes that influence the phylogenetic signal contained in genomes, and thus, groups defined by an averaged phylogenetic signal could be considered natural; however, there is no guarantee that they are only caused by shared organismal ancestryâ
I thought Irreducible complexity involves building something from scratch. My mistake if this is not accurate. Nevertheless, building viruses from scratch by a mind without life preceding it was what I was getting at.
You are forgetting that ,in the common design model, the origin of life is also supposed to be the origin of viruses.
For instance, there are three main hypothesizes on the origin of viruses with no clear explanation as to which one is correct:
- the virus-first hypothesis claims that viruses predate or coevolved with their current cellular hosts; 2. The progressive, or escape, hypothesis claims that viruses arose from genetic elements that gained the ability to move between cells; 3.the regressive, or reduction, hypothesis suggests that viruses are remnants of cellular organisms.
However, my model combines all three hypotheses. On the other hand, common descent model has nothing to offer in this area as well.
Origin of Viruses | Learn Science at Scitable (nature.com)
I never suggested that I knew this to be the case or else I would not need to be on this forum to argue my case. Just read post 326 in this source where I explain it in detail:
Can God be a useful âscientificâ hypothesis? Yes - Peaceful Science
Yes, it was a failed attempt at paraphrasing.
How can you say this when common descent does not have an origin of life model?
This is a bad example because my model accepts limited common ancestry.
Then, give me an article suggesting how evolutionary biologists consider pseudogenes to be functional rather than useless remains of once-functional genes.
You have that precisely backwards. The gaps in the record are mostly between very similar species. At higher levels, intermediates are frequent. And the transition to mammals is particularly well attested. The gaps are against you.
This still makes no sense, no matter how often you repeat it. HGT works only between already existing species. Whatever youâre talking about, it canât be HGT. You persist in using words with private definitions that nobody else knows.
How would you recognize these basic types? How do you distinguish between created similarities and inherited ones?
Since your basic types are of higher animals only, how is the origin of life or LUCA at all relevant?
Did you miss the part where he tells you that itâs irrelevant?
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Yet it was the âsourceâ quoted directly after your claim. If it âwas not the source [you were] referring toâ, then why did you quote it there?
And in doing so, you make it much easier to get the meaning of the original source completely wrong, particularly when your secondary source is a dishonest creationist quote-mine.
This is one of the reasons that many here consider any edifice built on such secondary sources to be utterly worthless. If you want to have any hope whatsoever of convincing anybody here, you need to refrain from the practice.
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So you didnât mean that dishonest quote-mine, you meant your other dishonest quote-mine.
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You are still misunderstanding because what I have been saying all along has nothing to do with convergent evolution. I have being talking about finding phylogenetic discontinuities or breaks in phylogenetic trees which is a testable prediction of the orchard hypothesis. When phylogenies of extant organisms are reconstructed, we donât see any breaks or discontinuities, effectively falsifying the orchard hypothesis. Its that simple.
This is you citing a paper you either didnât read or failed to understand. Please highlight any section in that paper where it shows that morphological data from fossils or living organisms rejects the hypothesis of shared ancestry?
This is not an answer. I repeat, how do you know God used HGT and viruses to do all the things you said he did?
The fossil record shows transitions from reptiles to mammals. It shows transitions from dinosaurs to birds. It shows transitions from aquatic to terrestrial life. These are observations in the fossil record that we shouldnât find if major groups of organisms were created separately. The fossil record refutes the orchard hypothesis and consolidates the common ancestry of extinct life forms that could fossilise and have been found. In addition when fossil data is incorporated into phylogenetic reconstruction, it improves the congruence of resultant trees.
I said there were gaps in the fossil record, but I never said they were gaps between major groups. In fact, there are lots of fossils showing transitions between major groups like that between reptiles and mammals which I mentioned. Look at this excerpt from Don Protheroâs book, Evolution - What the Fossils Say and Why it Matters, pg 89:
The fossil record betrays you.
This is dense nonsense. I bet you donât understand the implications of what you are saying. Letâs start from the top:
âAs I told you before, God used HGT to create basic types of organisms (or original kinds) with the highest amount of biochemical similaritiesâ
The molecular similarities among apes is far greater than that between apes and fish, so to say that God created these original kinds with the âhighest amount of biochemical similaritiesâ is downright nonsensical. That is, to get an original ape and fish kind, you would have to make both groups sufficiently different at the molecular level and not more similar. For example, pick any two humans, you would see that they share virtually the same biochemistry; pick a human and ape, the biochemical similarities are still vast but the differences are enough to delineate them as separate species; now pick a human and tuna it would become quite obvious that you would need relatively more molecular differences to delineate both species. Saying God made the original fish and ape kind or bird and insect kind with the highest amount of biochemical similarities is objectively moronic.
âThen, allowed those basic types to diverge into different kinds where those kinds became increasingly dissimilar and ,thus, it would explain the results of the study you gave me showing an increase of similarity between organisms as you go back in timeâ
You donât see what you are doing here? You want that these original kinds to extremely biochemically similar while wanting them to be sufficiently different as well. You canât have both, sorry. If there was an original fish kind, its biochemistry must have been sufficiently different (not extremely similar) to separate it from an ancestral ape kind.
In addition, you misunderstood that paper I cited which showed ancestral sequence convergence as one went back further in time using ancestral sequence reconstruction. Orangutans and gorillas shared a common ancestor, but ever since they diverged they have picked up sequence (proteins and DNA) differences. This means if we went back in time, the molecular sequences of orangutans and gorillas would coalesece into the molecular sequence of their common ancestor. The researchers did this for a wide range of protein sequences and there was coalescence or convergence, that is, the sequences became more similar to each other the further back they went in time explicitly showing common ancestry.
I think you conflated biochemistry (metabolism, enzymology, transcription, translation, gene expression regulation etcetera) with biochemical sequences, hence the ridiculous things you said above.
If these original kinds were created de novo then it means there was no way God would have used HGT to make them more similar, because HGT only happens between preexisting organisms.
More importantly, HGT that recapitulates the patterns of common descent is known to only happen between closely related species and not across distantly related groups. The original kinds are not related genealogically, that is, they are neither closely nor distantly related so you can kiss biased HGT goodbye as a mechanism of generating the illusion of universal common ancestry.
Oh my God. The paper literally says âthe observed phylogenetic pattern reflects both vertical inheritance and biased HGTâ. The original kinds postulated by the orchard hypothesis got their genes de novo, not through âvertical inheritanceâ making the findings of that study completely unhelpful to the orchard hypothesis.
HGT when biased by common descent will replicate the patterns of common descent, hence making it difficult to know when vertical inheritance is acting alone or together with horizontal gene transfer. The point you are missing is that there must be rcommon descent to bias HGT to replicate its patterns.
Yes they are separate but the authors tell us what makes HGT replicate the patterns of common ancestry and the answer is common ancestry itself.
Good, I boldened the part you are totally ignoring. HGT isnât acting alone, neither is vertical inheritance, rather both are acting together to generate that pattern and thatâs because the shared ancestry of the prokaryotes examined in the study is biasing HGT to recapitulate its patterns.
Does this lend support to the orchard hypothesis? No and thatâs because the original kinds didnât get their genes vertically (that is, from a preexisting ancestor) since they were made de novo, but according to the study HGT needs common descent (derived via vertical inheritance) before it can replicate its patterns and your original kinds didnât experience vertical inheritance.
Good. I boldened the part you are ignoring too. There must be common descent before HGT can recreate the patterns of common descent.
Of course if HGT (biased by common descent) is acting together with vertical inheritance (or vertical gene transfer) to create the patterns of common descent, then there would be some difficulty in determining the relative contributions of both.
Your misunderstanding of that paper is profound and it doesnât support the orchard hypothesis one bit.
LOL. De novo created things donât have ancestors. You canât grant that because its default by definition.
Has anyone here claimed LUCA was the first life? Has anyone here claimed universal common ancestry has anything to do with the origin of life? Stop building worthless strawmen.
The origin of life has nothing to do with our discussion on why we see a tree-like pattern in the data. If God created a single population of unicellular organisms similar to LUCA and caused it to evolve to all current lifeforms we would still see the tree of life pattern in the data.
The tree-like pattern in the data completely upends the orchard hypothesis.
You have a comprehension problem indeed. Didnât I write:
âThe tree-like patterns in the data can be due to shared ancestry alone or a combination of shared ancestry and HGT.â
Tell me how that conflicts with the part of the quote you emphasized in bold?
Why would you bring up irreducible complexity if you did not understand it?
A claim for which you have no evidence for.
Donât try to change the topic now. You claimed viruses need intelligence or the aid of intelligent life to infect cells but that is demonstrably false. All viruses need to infect other lifeforms are the various blind physicochemical forces.
Whether common descent has anything to say (it doesnât and has no need to) about the origin of viruses is irrelevant to our discussion. What matters is that common descent exceptionally explains the nested hierarchy of life, hence the tree pattern in the data. The orchard hypothesis, your model, is falsified by the presence of the tree pattern.
Thanks for admitting that all the things you have said here are unfalsifiable, since you donât know if God did it and he is the only one who can tell if he did any of that. There is no point in me further responding to unscientific and frankly nonsensical claims.
No its not bad paraphrasing. Its deliberately lying about a reference. You keep doing this and I wonder why moderators havenât done anything to stop this.
Common descent has nothing to do with the origin of life. It has everything to do with the nested hierarchy and tree pattern in the data, which has being the focus of our discussion for crying out loud.
It is not a bad example and since your model accepts limited common ancestry, it is falsified because we see universal common ancestry in the data. Humans and other apes are related. Apes and other monkeys are related. Monkeys and other mammals are related. Mammals and reptiles are related, and both are related to insects, fish and others. These relationships go back until all life is genealogically linked.
Your amnesia is back. You claimed that we expect to see many pseudogenes under common descent and I explained why that wasnât a prediction of common descent, but how the distribution of those pseudogenes (regardless of their number) in descendants was. I didnât say anything about pseudogenes being functional or not. Another irrelevant response from you.
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I canât speak to the coherence his private mental state, but this would be the most coherent way to make sense of his claims. I think this is what he is aiming at, but is struggling to find the right words to state clearly.
The issue, it seems, is that he is mixing categories. HGT is a mechanism that creates homoplasy, but what he really means is that separate creation would produce more homoplasy than common descent. That is close to your understanding too.
What is helpful is that he puts an estimate on it, 50%, which is at least in the direction of a falsifiable hypothesis. We can test that with DNA, and weâll find that this hypothesis is ruled out. Of course, that 50% is a ball park, and other numbers might work too. For humans-apes, a clear positive control, weâd get something less than 1% right? That doesnât seem to be anywhere near what weâd expect from separate creation.
Since he wonât identify any âbasic typesâ, Iâm not even sure that humans and apes are supposed to belong to different ones. The jello persistently refuses to be nailed to the wall.
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HGT is most often detected by strong conflict with tree-like patterns in the sequence data. IOW, HGT results in a lack of a nested hierarchy. What do we see in real world biology? In eukaryotes, we see a really, really strong signal for a nested hierarchy with very little evidence of HGT in the vast majority of clades. The presence of this nested hierarchy refutes your HGT argument.
As a counterpoint, we have the GloFish:
These are designed fish. They carry fluorescent protein genes copied straight over from jellyfish and other distantly related species. If we compared the GloFish green fluorescent protein genes with the genes from jellyfish the sequences would show striking similarity. We would also not find those same genes in more closely related fish, or even in any other vertebrates. The fluorescence genes would not fit into a nested hierarchy. This is why a nested hierarchy points to common descent because this is the pattern that common ancestry produces and common design and HGT does not.
Then there is no reason we would expect those original kinds to fit into a nested hierarchy, AND YET THEY DO.
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Based on certain simulations, it seems HGT can also reproduce a nested hierarchy. Thus, it seems his argument is that since HGT can remake those patterns of common descent, God used it to transfer genes between the original kinds, hence creating the illusion of universal common descent. However, he doesnât seem to realize that HGT replicates patterns of common descent because of common descent.
Which simulations are these?
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From here:
I was not referencing the study on that claim but on another claim of yours:
" In addition when fossil data is incorporated into phylogenetic reconstruction, it improves the congruence of resultant trees."
I already explained this in post 136. I made some edits on it to be more clear.
I am not sure what makes you say that. All it takes is one or two genuine discontinuities in series and Universal common ancestry is falsified. Therefore, pointing out examples that seem to support common ancestry does not do you any good.
I beg to differ. If you Watch this video from 47:30-50-30, an actual expert in the field will explain to you why the fossil record has failed you:
Gunter Bechly vs Joshua Swamidass - For and Against Intelligent Design - YouTube
Somewhat Yes. The differences would mainly come from morphology though NOT phylogenetics for the millionth time.
Whoa, I was talking about biochemical sequences when I said this not biochemistry.
I am not sure where I misunderstood their paper here. This is basically what I was explaining as to how my model fits the data
Then, let me be more clear to help you understand why I did not conflate the two. Under the common design model, Viruses were designed by God to be the first life and it was the means to create unicellular organisms like bacteria from the deep sea hypothermal vents. In addition, those different species of unicellular organisms would undergo a heavy amount of HGT from those viruses to give them those similarities.
Then, those microbes would be used ,as parts to a car, to assemble basic types of advanced life from different locations and times around the world, such as apes and humans or fish and birds. After this, vertical inheritance would be the dominate way in which advanced life swaps genes. This would explain the data in your study and the study I provided on HGT.
Thus, this is why I grant that there would naturally be an appearance of universal common ancestry coming from phylogenetics that does not look like separate creation compared to what we in the fossil record.
Good, I boldened the part that I donât agree with and reject because you have not provided support for this in their paper. The quote you did provide was referring to something else as I mentioned before.
Well, the preexisting ancestors in my model would naturally be unicellular organisms rather than other advanced life. So even if you found a quote from their paper that supported your contentions, I donât see where there would be a conflict in my model. Unless you are applying this objection to unicellular organisms instead. But, I still donât see where the conflict would be if common descent does not include the first life.
I boldened the part that you are also misrepresenting because it does not specifically say what you are claiming .
In that case, you are attacking a strawman like you did with the GLO gene. I have made it very clear that we would not expect biochemical differences because of the mechanisms and motives of God that were involved.
No, God created viruses. Then, used those viruses to create unicellular organisms.
From the study I already provided to you:
"The virus was created by genome sequencing pioneer Craig Venter and his team at the Institute for Biological Energy AlternativesâŚ
âŚVenterâs team cobbled together the virus, called phi-X174, following its published genetic sequence. They stitched up its DNA from ready-made overlapping fragments called oligonucleotides, each built from 40 chemical building-blocks, or bases."
Not quite, I am saying that they need a mind to manipulate and make profound changes to cells as suggested by experiments and observations that I showed you already.
Whatever. I never suggested this in my comments.