But it doesn’t really hurt as long as the science is honest, does it? I’d be pretty excited if we got to a point where people basically agreed to all the observations and we just had varying theological/philosophical positions on the why and how (not the scientific how). Does it really matter if some people think that every mutation is an intentional act of God? Or if people think life and the universe where a cosmic pool shot or just not special in any way, devoid of anything remotely supernatural?
Surely adding God to an otherwise fine hypothesis just makes it needlessly complicated from a scientific point of view, it doesn’t make the scientific part of the hypothesis suspect or wrong, does it?
But why is he trying so hard to sell the idea to scientists who, as you say, are likely to see it as needlessly complicated? (Rhetorical question, no answer is expected).
Words fail. Literally. Night is day, ignorance is strength, freedom is slavery. Basic types (a recent entry into your vocabulary) include multiple kinds, and so do species. How species relate to basic types or what any of those words actually mean is elusive. Words seem to have private meanings, and those meanings are not fixed. It’s impossible to know what you mean.
Do you realize this makes no sense? De novo created organisms don’t have ancestry, so there can’t be half vertical inheritance and half HGT.
We already have a pretty good sense of the depth of HGT. Its pervasive among prokaryotes (especially among bacteria), and becomes more infrequent as you approach multicellular eukaryotes. For multicellular eukaryotes in general, the signal of common descent is not seriously affected by HGT. Among prokaryotes, however, HGT is more pronounced, but the signal of common descent is still strong in genomic data. Why do you ignore this data, like the one in the paper below?
Grrrr. I was addressing the findings in that “biased gene transfer” paper you cited. One of such findings was the seeming absence of HGT in higher taxonomic levels across Bacteria, but its commonness among lower taxonomic levels. If this detail made any sense to you, it would have prevented you from citing this paper in the first place to show that HGT is the cause of the pattern of common descent in all organisms. I knew prior to making that comment that prokaryotes and unicellular eukaryotes have transferred genes to vertebrates and invertebrates and this happens at significantly lower rate relative to prokaryote-to-prokaryote transfers.
You have failed to address my question on what explains patterns of common descent between us and other great apes since we don’t engage in HGT with each other.
You are confused man. You initially claimed HGT accounts for the observed patterns of universal common ancestry, then you backtracked saying its probably half vertical and half horizontal (which is ridiculous for supposedly de novo created organisms), and now you have returned to your initial stance which is false.
If this claim of yours is based on the quote from that paper, then you have misinterpreted that paper. It doesn’t say its either vertical inheritance or horizontal gene transfer as you do, it says its both for the prokaryotes it examined. It says biased HGT recapitulated the patterns of common descent (as opposed to muddling it) on a large scale in the sequences examined. Let’s go through the Results section and see what went down.
First, they detected the participation of HGT in the evolution of the Tyrosine aminoacyl-tRNA Synthetase (TyrRS) in the genetic sequences they examined.
Now let’s see what they did in the study to figure out the effects of HGT on recovering the tree-like signal due to vertical inheritance in the data:
In the above, they are hypothesizing that biased HGT will reproduce or maintain patterns produced by vertical inheritance/common descent/shared ancestry. In contrast, unbiased HGT should erode the pattern of common descent in the data.
They tested this hypothesis using a simulation. They started with randomly generated unbiased HGT events (50 in number) and as predicted, these unbiased HGT events reduced the visibility (“loss of correlation”: decrease in R^2) of the pattern of common descent:
They went on to test the effect of biased HGT, using 250 simulated events. As predicted, these biased HGT events maintained (“increase in R^2”: R^2 is the correlation coefficient) the phylogeny derived from the 16S rRNA sequences, that is, they did not erode the signal of to shared ancestry, but reproduced it:
I hope this was clear enough and I hope it corrects your impression that the signal of common descent is illusory in prokaryotes. Its there, but HGT will tend to mar or keep it.
Just cite the evidence. If you are going to give me quotes, don’t bother.
This is absolute nonsense. Under common descent, descendants get what their ancestors pass on to them. If functional genomic elements are widespread in an ancestral population, lineages that emerge from that population will most likely have them as well and vice versa.
Were they also terrestrial but aquatic? Migratory but sessile? Bipedal but six-legged? Nocturnal but phototrophic? Gigantic but microscopic? We already know they had mutations that were both beneficial and neutral.
No, you just misunderstood what I said. I meant that 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.
Yes, it was my mistake for not being more clear. I meant de novo created organisms for advanced life NOT simple life:
A Universal common designer re-used a DNA blueprint, RNA viruses, and chemical constituents to separately construct animals from different locations around the globe.
I think I clarified my point above. I am not suggesting that HGT accounts for EVERY phylogenetic pattern. Of course, there is going to be a certain amount of common descent patterns we see since my model expects it. It just would not be universal, which is what I am arguing against.
How do you know that HGT did not play a part in creating those similarities instead?
Again, that is not the only thing it does. HGT also produces the same effect we see in common ancestry. I don’t understand why you keep ignoring this part of the study I gave you since it is really important.
RNA viruses are irreducibly complex and cannot propagate without a host or intelligence. For this reason, it would require the designer to continuously create viruses to have them evolve into bacteria from within deep-sea vents AND force those bacteria to evolve further from other created viruses. As a result, this would require multiple origins, which happens to be consistent with current observations while common descent has no model for the first life.
The Phage-assisted continuous evolution (with the apt acronym “PACE”) is example of what I mean.
What you are saying does not make any sense. Psuedogenes are supposed to be copying errors where function has been eroded by random mutations.
I already explained in previous topics that this contradicts God’s personal nature. He could not do this anymore than he could create a square circle or sin.
This sounds like atheistic evolution to me not my model.
And it seems that you want to pretend that materialism is true, but instead it has been falsified.
I clearly understood your claim, and you go right ahead to repeat it immediately after this. Your level of ignorance and misunderstanding is simply outstanding.
Unfortunately for this claim, there is no evidence for the existence of these “basic types”. When we look at the fossil record and mostly at the molecular data, universal common ancestry is what see. I have presented this evidence on many occasions to you but you have consistently ignored it.
What you don’t realize is that this statement is testable. If multiple, basic types of organisms were created and were allowed to diverge, becoming increasingly dissimilar as time progressed, it means that if we went back in time using phylogenetic reconstruction we would see convergence until we arrive at those basic types. Thus, if the separate origins hypothesis were true, we should see this orchard pattern (on the right in the figure below) in phylogenetic trees:
In contrast, if UCA is true, we should see the tree pattern on the left (in the same figure above).
For example, if there was basic dog kind and a basic ape kind some time in the past and both underwent evolution producing all dog kinds and ape kinds today, when we reconstruct their evolutionary histories, they would remain separate. However, when we do the phylogenetic reconstruction, they don’t remain separate, instead, they coalesce at some point in time into an ancestral population. In the data, mammals, birds, fish, reptiles, insects etcetera all coalesce into an ancestral population if we go back far enough to the time of their last common ancestor.
The orchard hypothesis doesn’t stand up to the data.
This is pure fantasy. The data says otherwise. In addition, you are yet to provide evidence that God did not employ common descent as opposed to separately creating your so-called basic types.
“Certain amount of common descent patterns”? That is terribly false. Datasets literally reek of common descent and since your model predicts limited common ancestry its wrong because we find UCA instead.
HGT means transfer of genetic material between distantly or closely related species. Humans, chimps and other great apes don’t do this with each other.
Its obvious my effort to help you understand that paper was futile, because your misunderstanding clearly remains.
According to that paper, biased HGT should mimic the patterns of vertical descent/shared ancestry/common descent when biased by shared ancestry. The hypothesis was tested via simulation and it panned out. So there was both a vertical and horizontal component for the organismal sequences used in this study. In contrast, your model deals with basic types or de novo created organisms with no ancestry (no vertical component), making this study unsuitable for you to use or cite.
Also, despite the pervasiveness of unbiased HGT among prokaryotes, the tree pattern can still be recovered from the tangled web created by unbiased HGT (thanks in part to HGT biased by vertical descent as shown in the paper you cited and the one I cited as well). UCA still wins my friend.
The furin CS of SARS-CoV-2 (an RNA virus) was genetically inactivated in several experiments, but the virus was still able to infect cells. So much for the irreducible complexity of RNA viruses.
I know viruses cannot propagate without a host, but they don’t need intelligence to propagate when they eventually find a host. Blind physicochemical (electrostatic and hydrophobic interactions for example) forces have been observed to be sufficient for the initiation and completion of the life cycle of viruses.
If bacteria evolved from viruses, we should see that on a phylogenetic tree. We don’t, making this claim false. More importantly, viruses don’t fit into the nested hierarchy that unites all living organisms.
You keep on making definite statements about how the designer acted. How do you know the designer used deep sea vents to create bacteria? How do you know he didn’t create bacteria on land or in the air?
Keep on fantasizing. I have shown you papers where common descent is explicitly tested against separate origins, with the former always coming out on top, but you keep ignoring them. “Current observations” are fully in support of common descent. Here is quote from one of those papers again:
Bolds and curved brackets mine.
PACE experiments have absolutely nothing to do with this.
Pseudogenes are passed down from parents to offspring, at the individual and population levels, so are genes. If an ancestral population has 1000 pseudogenes, lineages that emerge from that population will also have that amount of pseudogenes (provided things like rapid divergence that erase sequence similarity of the pseudogenes to their functional paralogs don’t occur). If another ancestral population has 200 pseudogenes, that’s what its descendant lineages will get. In summary, descendants get whatever their ancestors have to offer be it pseudogenes, functional genes, transposons, ERVs etcetera.
That this makes no sense to you makes exposes your deep-seated misunderstanding of evolution.we
Well, they probably did once. There may have been some hybridization between the human and chimp lineages for a while after general separation. And there’s always transfer by vector to consider, though I know of no examples in the human genome.
What I don’t understand is what HGT has to do with separate creation. Is he talking about HGT as a metaphor for copying sequence from another species into the new creation’s prototype genome? Because regular HGT is between organisms that already exist. And what would be the point of creating a brand new genome to specification only to introduce foreign genes directly afterwards?
Yes that’s likely, but I haven’t seen any evidence in support of that hypothesis.
Yes and I think it would be the most plausible route for HGT between primates, even if it rarely occured. In any case, HGT does little or nothing to help explain the patterns of common ancestry for the great apes.
He thinks that because biased HGT can recreate patterns of common ancestry, that it explains why you can have separately created kinds and still see the illusion of common descent. What he doesn’t realize is that HGT events which mimic/reproduce/recreate patterns due to common ancestry are biased by shared ancestry itself, per the study. Hence, that paper and its findings are completely irrelevant to his separate origins model wherein the original kinds don’t have ancestors.
No, we would see the same phylogenetic-treelik pattern for advanced life from the common design model, as I keep telling you, because of the motives and mechanism of the designer (Unless you are including simple life when you said this).
However, we would expect to see the orchard hypothesis reflected within the fossil record, which leads me to the next thing you said…
Read the source below that supports these claims:
“Given the fact of evolution, one would expect the fossils to document steady change from ancestral forms to the descendants. But this is not what the paleontologist finds. Instead he or she finds gaps in just about every phyletic series. New types often appear quite suddenly, and their immediate ancestors are absent in the earlier geological strata. The discovery of unbroken series of species changing gradually into descending species is very rare. Indeed the fossil record is one of discontinuities, seemingly documenting jumps (saltations) from one type of organisms to a different type.”
From “What Evolution Is” Ch.2
“Eldredge and Gould not only showed that paleontologists had been out-of-step with biologists for decades, but also that they had unconsciously trying to force the fossil record into the gradualistic mode. The few supposed examples of gradual evolution were featured in the journals and textbooks, but paleontologists had long been mum about their “dirty little trade secret:” most species appear suddenly in the fossil record and show no appreciable change for millions of years until their extinction.”
Right, this is another one of the many abilities HGT can do that the paper argued. But, this was not the crux of the paper. If you actually read the discussion, you will see them reiterate my point:
“We have shown three lines of evidence for preferential gene transfer having the potential to create phylogenetic patterns comparable with those generated by shared ancestry. These transfers are characterized by the preference of taxa to exchange genes with partners more similar to themselves rather than rare HGTs that may occur randomly and indiscriminately.”
The last thing they said shortly after this was what you said about HGT maintaining patterns among closely related organisms but they did not suggest that this negated or refuted their main point.
Now, they did suggest that this applies mainly to microbes but this would only reinforce what I said earlier about seeing the same phylogenetic tree-like patterns from a common design model as well. I explain further below.
Scientists were successfully able to synthesize the RNA molecules of a virus and reconstruct a virus particle from scratch [1]. In addition, scientists were able to construct self- replicating RNA in the laboratory as I showed before. More importantly, functional RNA sequences or RNA viruses have not yet been observed in nature to self-replicate without the help of other living things or intelligent life. Therefore, RNA viruses were developed within the pool of self-replicating RNA sequences by an intelligent agent, which I explained already can only be identified as a transcendent cause.[2]
However, the main reason why I believe this agent most likely created and designed the first life to be viruses is because they not only display elements of functionality, but look as if they perform important and overarching purposes in ecosystems that could only be done by an intelligent designer according to PACE experiments. [3]
Now, here’s a model as to how the first life probably came about based on observations that seem to be consistent with experiments:
Before the leftover meteorites, which contain amino acids, were clumped together to form the “formless” earth 3.8 billion years ago after the late bombardment event, this conscious agent developed virus-like RNA molecules within the “void” of the earth inside the deep-sea oceans in order to create unicellular organisms [4].
For example, 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 [5]. 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 world’s oceans compared to any other micro-organism and cover every ecological niche around the globe [6]
Finally, these viruses that become bacteria and archea would be used as a carrier for information of different genotypes from HGT in order to initiate design diversity around the globe [7]. This would explain why microbial organisms that have been fully sequenced show no clear pattern of common descent from an analysis of the tree of life at its most basic level [8]. For example, certain species of Archea bacteria are more closely related to species of eubacteria or common bacteria than they are to members of their own kingdom. [9]
Thus, We would not expect a treelike pattern according to my origin of life model but multiple origins . This would explain why and how humans share the appearance of universal common ancestry where we have similar biochemical and morphological features among the animal kingdom because we understand the motives and the mechanisms of the designer. Remember, common descent does not have an origin of life model.
“Evolutionary biologists consider pseudogenes the dead, useless remains of once-functional genes. According to this view, severe mutations destroyed the capacity of the cell’s machinery to read and process the information contained in these genes.”
Except that, as I demonstrated above, that chapter does not in fact support your claims. Meyr goes on immediately after this dishonest quote-mine to explain why “the fossil record fail[s] to reflect the gradual change one would expect from evolution”.
Have you read the full chapter@Meerkat_SK5? If not, then please do not pretend that you know what it actually says, let alone what it does or does not “support”.
Again, this is why I (along with a good many others on this thread) consider an edifice built on such quote-mines to be utterly worthless.
Beyond that, even if you had articulated Meyr’s view correctly, it would still be only that – one scientist’s opinion – not scientific evidence.
You don’t seem to understand the implications of the orchard hypothesis. I will go at it again.
If basic types of advanced lifeforms (like an “original” ape kind) were created de novo, then we expect to find no genealogical connections between the present day apes and other organisms in the biosphere. In other words, we expect to see a break or discontinuity in phylogenetic trees for apes and other organisms.
However, if a group of organisms like the apes shared a common ancestor with a different group, say fish, then we would expect to find a genealogical relationship between both groups on a phylogenetic tree. In other words, there will be no discontinuities between fish and apes.
The above hypotheses are testable and can be evaluated in a number of ways. Sequence (from proteins and DNA) data has been extensively used to test both hypotheses and only common descent has survived scrutiny so far. Tests using morphological data from extant and extinct (fossil) organisms have also failed to reject the hypothesis of shared ancestry. Morphology and molecules tell us we are all branches in one big tree (or net) of life.
As to the motives of the designer, how do you know them?
The fossil record betrays you as well on at least two counts. First, when integrated into phylogenies, it improves congruence and reinforces the patterns of common descent. Second, if reptiles and mammals, for example, were separately created then we should not find transitional fossils between both groups. We do find transitional fossils for both groups and a lot at that! Older fossils tend to look more reptilian, while younger fossils tend to look more mammalian beautifully illustrating the progression of evolution from reptile ancestors to mammalian descendants.
Yes there are gaps in the fossil record, but the number of fossils found and examined in the fossil record so far are enough to tell us that evolution happened. In the fossil record, we see mammals evolve from reptiles, birds evolve from dinosaurs etcetera. Don’t even get me started on molecular fossils.
Where in that material is evidence that God did not use common descent to create all lifeforms?
Where is the evidence in the above quote that God did not use common descent to generate all lifeforms?
Again, where is the evidence in the above quote that God did not use common descent to generate all lifeforms?
Yes, the ancestors of Homo sapiens of Eurasian descent who left Africa interbred with Neanderthals, and got a bit of their DNA, but the amount of acquired DNA is too small to account for the staggering similarities between Sapiens and Neanderthals. I specifically asked about chimps, gorillas and other great apes who are not hominins, but you are yet to explain the vast amount of shared similarities they have with us since we don’t engage in HGT with them. Explain it.
You are grossly misunderstanding that quote and the rest of the paper. Look HGT can erode phylogenetic patterns due to shared ancestry, but if HGT is biased by shared ancestry, it will tend to reinforce patterns created by shared ancestry. In other words, HGT can’t produce patterns similar to those due to shared ancestry in the absence of shared ancestry or common descent. They say this right there in the Introduction:
When does biased HGT produce patterns similar to shared ancestry? Read it from them:
According to the authors, there must be common descent and it must bias HGT before HGT can replicate or mimic its patterns. When common descent doesn’t not bias HGT between closely related taxa, it erodes the phylogenetic signal as opposed to mimicking it.
The original kinds in your orchard model don’t have any ancestry, talk more of shared ancestry, so HGT will not generate the same patterns of shared ancestry for them because there is no common descent to bias it.
Their data provides no support for your model because it lacks shared ancestry which seems necessary to bias HGT to replicate patterns associated with it.
The tree-like patterns in the data can be due to shared ancestry alone or a combination of shared ancestry and HGT. It lends your model no support.
What has this got to do with the supposed irreducible complexity of RNA viruses? You are as confused as ever.
Viruses replicate in all life forms (including other viruses too) regardless of the depth of their intelligence. Bacteria, fungi, protists, etcetera aren’t intelligent but they are persistently infected by viruses. Viruses employ chemistry and physics to infect living organisms, no intelligence required. You really need to get better science education, because you have a really distorted view of basic virology.
How do you know viruses formed this way? And how do you know an intelligent mind was involved in the process?
Um viruses kill cells they successfully infect and that is basically what they do. This killing can happen immediately or after a long time. Haven’t you heard that viruses are obligate parasites? That’s why bacteria, for example, had to evolve mechanisms (like the CRISPR system) to deal with viral infection. For sure viruses have been beneficial in many ways to the biosphere, but they would have to destroy organisms to render those benefits.
In addition PACE has nothing to do with the origin of life or viruses. Can you stop inappropriately referencing it?
So you are telling me God went through all this stress to create life when he could have poofed life into existence. In any case, how do you know God really did any of these things you claim?
In addition, all of the references do not consider the intelligent design hypothesis for the OoL. They are seeking naturalistic explanations for that. Citing them to show support for an idea they are not arguing for is serious misconduct.
Your reference says nothing about viruses becoming Archaea or Bacteria. You are deliberately misrepresenting that reference.
HGT muddles the phylogeny of microbes but the tree pattern is still there. Even the biased gene transfer paper you cited showed the tree pattern derived from the 16S rRNA sequences due to vertical inheritance. Its also odd that you cite a 1999 paper when there are more recent papers like the ones below which show the tree signal can be extracted despite the presence of intensive HGT in the evolutionary history of prokaryotes.
We fit into the nested hierarchy of life because of common descent, similar to the way you and your siblings fit into your family tree because of common descent from your parents. I bet that if I argued that your family tree is illusory and that you were separately made by aliens who designed you in a way that fits that family tree, you would call me crazy. More importantly, the patterns due to vertical inheritance in your genome would be a certain way and that’s how you would know if you are truly a descendant of your parents.
Another completely irrelevant quote. We inherit pseudogenes, genes, and other genetic material from out ancestors. The number we inherit is irrelevant, what matters is the pattern of inheritance.
Even if that quote-mine was actually Mayr’s view it still wouldn’t support @Meerkat_SK5 because that snippet suggests common descent with tinkering, not orchard-like common design.
