Exposing the evolution theory. Part 2

Kleinman:

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So, the physics and mathematics of the Kishony and Lenski biological evolutionary experiments are not evidence?

AZPaul3:

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Not your errant interpretations, no.

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So the layman is now going to give his errant interpretations of the physics and mathematics of the Kishony and Lenski biological evolutionary experiments, no.

sensei:

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Many things produce nested hierarchies. Keep ignoring that fact and proving your utter ignorance.

top.Tanypteryx:

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And yet you have not been able to provide supporting evidence for even a single one, no matter how many times we ask.

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Tell us more about how a germ cell line can get 200,000 retroviral infections without killing that line. Don't you know that Taq posted an example of koalas that may go extinct from a single retroviral infection?

Tanypteryx:

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Still Conman the Bullshit Peddler, I see. Still no new citations of your Bullshit papers?

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Is that your best response? You certain can't explain the Kishony and Lenski biological evolutionary experiments. That would require that you have some scientific training.

Dredge:

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AZPaul3:

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Like sensei, are you claiming there are biological populations that evolve in other than such a pattern?
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Whether we have the level of perfect information that would allow me to write a paper for you detailing pre-Cambrian and Cambrian patterns or not is unimportant (AI available). What would be important, world shattering, conclusively revealing, is if you show us one of these majik biological lineages that violates the nested hierarchy.
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Got any? Only takes one.

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The layman still can't explain the simplest biological evolutionary experiments. But that's not surprising, neither can biologists.

Kleinman:

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So, the physics and mathematics of the Kishony and Lenski biological evolutionary experiments are not evidence?

Taq:

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The populations in those experiments produced a nested hierarchy due to common ancestry and evolution.

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You are partially correct. The Kishony and Lenski biological evolutionary experiments do produce a nested hierarchy. Here is a video of the Kishony experiment that demonstrates that:
The Evolution of Bacteria on a “Mega-Plate” Petri Dish (Kishony Lab)
At time 1:42, the presenter actually draws in the nested hierarchy (family tree) for this example of the evolution of drug resistance.What this video and experiment do not demonstrate is the concept of (universal) common descent which you and other biologists try to imply with your nested hierarchy drawings of reptiles and birds, and fish and mammals.The Kishony and Lenski experiments demonstrate how slow descent with modification and adaptation works. You claim that sexual reproduction and recombination overcome this. However, what you are not considering is that if adaptive mutations must occur in a single allele, recombination will not make a difference.Consider this example, it takes 5 mutations to give a high-efficiency beta-lactamase allele (high resistance to penicillin class drugs) bacteria variant. Even if the bacteria can recombine, it will make no difference in the evolution of that allele. Recombination only accelerates biological adaptation when adaptive alleles can recombine and the probability of that happening depends on the frequencies of those adaptive alleles. But recombination will not accelerate biological adaptation if the accumulation of adaptive mutations must occur in a single allele. Your claim that humans and chimpanzees are related is not reasonable. There are too many genetic differences, even if we use your numbers. You are making an unreasonable extrapolation when drawing your nested hierarchies.

Kleinman:

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Tell us more about how a germ cell line can get 200,000 retroviral infections without killing that line.

Taq:

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The same way you survive with 200,000 retroviral insertions in your genome. These insertions are a fact.

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I'm very surprised by you when you make this claim. Are you really a virologist? Aren't you aware of what HIV does to an untreated person with this infection? And your own link about koalas and the retroviral infection these animals have may drive them to extinction. Yet you seem to think that a lineage can get 200,000 of these infections when a single infection has such great lethality. I think you are having trouble recognizing what a fact is and what a misinterpretation of data is because this is a gross misinterpretation of the data by you.

Kleinman:

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And your own link about koalas and the retroviral infection these animals have may drive them to extinction.

Taq:

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The exogenous retrovirus may drive them to extinction, not the endogenous ones.
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You have over 200,000 endogenous retroviruses in your genome. This is a fact. You survive just fine with those ERV's

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An endogenous retrovirus must start as an exogenous retrovirus causing an infection. Your own koala example demonstrates this and may drive them to extinction. Now you want to claim that a lineage can have 200,000 of these infections (even if each infection is separated by 10s, 100s, or 1000s of generations) and it never kills that lineage, even when the data shows the lethality of these viruses in a single generation. You and the authors of any papers making this claim are misinterpreting the data, just like you misinterpret the data of recombination.

Kleinman:

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Your own koala example demonstrates this and may drive them to extinction.

Taq:

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Some retroviruses may pose a serious threat to a species, others may not. It depends on the virus.

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So what is your claim now? Only 100,000 of the 200,000 infections pose a serious threat? Or 50,000? Or 25,000? It only takes one to be a serious threat, and your koala example shows it only takes one.

Kleinman:

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Now you want to claim that a lineage can have 200,000 of these infections (even if each infection is separated by 10s, 100s, or 1000s of generations) and it never kills that lineage,

Taq:

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You are living proof that this occurs. You have 203,000 ERVs in your genome.

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It would never enter your mind that none of these sequences are the result of retroviral infection. Don't humans and chimpanzees have sequences that control DNA transcription?

Kleinman:

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You and the authors of any papers making this claim are misinterpreting the data, just like you misinterpret the data of recombination.

Taq:

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I'll stick with the experts on this one.

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Do you mean those so-called experts that can't explain the physics and mathematics of biological evolution and fail to explain why drug resistance evolves and cancer treatments fail? Your so-called experts are failures that don't understand that a single retrovirus infection can be fatal to a lineage.

Kleinman:

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Only 100,000 of the 200,000 infections pose a serious threat? Or 50,000? Or 25,000? It only takes one to be a serious threat, and your koala example shows it only takes one.

Taq:

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Are you dying because of the 203,000 endogenous retroviruses in your genome? No?

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Taq, you don't know if the sequences are the result of retroviral infections. All you have demonstrated is that a single retroviral infection can be fatal to a lineage with your koala example.

Kleinman:

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It would never enter your mind that none of these sequences are the result of retroviral infection.

Taq:

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That's like a defense attorney trying to convince the jury that fingerprints at a crime scene never came from his defendant's fingers. They aren't even fingerprints, they are just some swirly marks that leprechauns made, right?

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Are you claiming that you have an exact match? Not a base differs between humans and chimpanzees? And all these examples are retroviral infections despite the fact that a single retroviral infection can be lethal to a lineage? You are seeing the wrong fingerprints.

Kleinman:

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Do you mean those so-called experts that can't explain the physics and mathematics of biological evolution and fail to explain why drug resistance evolves and cancer treatments fail? Your so-called experts are failures that don't understand that a single retrovirus infection can be fatal to a lineage.

Taq:

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You don't even understand how the basics of meiosis work. Sorry, but I will go with the experts on the Human Genome project, all of whom have way more knowledge and experience than you do. We could even go with the guy who wrote the textbook on retroviruses:

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You wish I don't understand how meiosis works. Your so-called expert doesn't understand that a single retrovirus infection can be lethal to a lineage. Your koala example demonstrates this, HIV demonstrates this, and many other retrovirus infections demonstrate this. Now you want us to believe that a lineage can get 200,000 retroviral infections (or 100,000, or 50,000, or you name it) and the lineage survives just fine. You need to learn the physics and mathematics of biological evolution and how biological competition, descent with modification and adaptation, and recombination works. And so does that author that writes a textbook that makes irrational claims. Why can't you explain how drug resistance evolves or why cancer treatments fail? Or why can't biologists explain how the Kishony and Lenski biological evolutionary experiments work? You are too busy hooked on this idea that a lineage can get thousands of retrovirus infections and everything is just fine. You and your so-called experts are wrong!

Kleinman:

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Taq, you don't know if the sequences are the result of retroviral infections.

Taq:

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We know that ERV's are the result of retroviral infections in the same way that we know fingerprints are the product of fingers.

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It is very easy to duplicate a fingerprint. All you have shown is that a single retroviral infection can be fatal to a lineage.

Kleinman:

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You wish I don't understand how meiosis works.

Taq:

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You don't understand how meiosis works. You can't understand how alleles in two different genes relate to one another in sexually reproducing species. Can you even tell us what the difference is between unlinked and linked genes?

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If you know so much about alleles, explain how drug resistance evolves and why cancer treatments fail. Explain why combination therapy works in the vast majority of cases despite the fact that many of these replicators do recombination. If you actually had an understanding of biological evolution, you could do this.

Kleinman:

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Your so-called expert doesn't understand that a single retrovirus infection can be lethal to a lineage.

Taq:

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What's the mortality rate for adenoviral infections?
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What's the mortality rate for HTLV-1 infections?

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You should know that adenovirus is not a retrovirus that normally causes mild symptoms but can kill under some circumstances. HTLV-1 is a retrovirus that is oncogenic. So, what is your point? Are you going to claim that a lineage can get 200,000 HTLV-1 infections and the lineage is just fine? There are lots of viruses that can be incorporated into the human genome, you can start with the herpes family. They cause many problems such as recurrent herpes cold sores, shingles, or recurrent Epstein-Barr infections (usually called Mononucleosis). But your claim for retroviruses is that they get incorporated into germ cells where viral infections in the early stages of pregnancy are oftentimes catastrophic for the fetus because they disrupt the differentiation process. I'm surprised that a virologist understands so little about what viruses do to their host.

Kleinman:

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All you have shown is that a single retroviral infection can be fatal to a lineage

Taq:

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I have 203,000 examples of non-lethal ERVs.

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This argument would convince anyone that had no idea what a virus does to its host, especially when the infection is in a germ cell.

Kleinman:

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If you know so much about alleles, explain how drug resistance evolves and why cancer treatments fail.

Taq:

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Already did that in this thread:
https://www.evcforum.net/dm.php?control=msg&t=20319

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You should publish it because biologists don't know how drug resistance evolves and why cancer treatments fail.

Kleinman:

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You should know that adenovirus is not a retrovirus that normally causes mild symptoms but can kill under some circumstances.

Taq:

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It also occasionally inserts into the genome. HTLV-1 is a retrovirus, and in most cases is asymptomatic.

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Does adenovirus insert into the genome of a germ cell, and what does it do to that developing child? It only takes one case to be symptomatic, and what do viral infections do to a germ cell? Have you ever seen the birth defects of a child that contracts a viral infection in the womb? And now you want to claim that a germ cell line can get 200,000 infections and the lineage is just fine.

Kleinman:

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Are you going to claim that a lineage can get 200,000 HTLV-1 infections and the lineage is just fine?

Taq:

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I have 203,000 pieces of evidence that it can.

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Does that evidence include what a retrovirus is doing to koalas, or what HIV does to humans?

Kleinman:

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But your claim for retroviruses is that they get incorporated into germ cells where viral infections in the early stages of pregnancy are oftentimes catastrophic for the fetus because they disrupt the differentiation process.

Taq:

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Koala embryonic development is not disrupted by the presence of these retroviruses. Your embryonic development was not interrupted by the 203,000 ERVs in your genome.

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Then, why are koalas threatened with extinction because of their retroviral infection? The author of the paper said this was a possibility. And you still haven't explained how a germ cell lineage can get 203,000 retroviral infections and the lineage does just fine. I expect your explanation will be just as good as your explanation of how drug resistance evolves and why cancer treatments fail.

Kleinman:

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This argument would convince anyone that had no idea what a virus does to its host, especially when the infection is in a germ cell.

Taq:

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You are the one who has no idea what the virus does to the host. For example:
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"But your claim for retroviruses is that they get incorporated into germ cells where viral infections in the early stages of pregnancy are oftentimes catastrophic for the fetus because they disrupt the differentiation process."
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Koalas with recently inserted ERVs are not born with catastrophic birth defects.
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You are wrong.

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Are you really a virologist? Do you really understand what a virus does to a host cell? Why don't you tell the readers that a virus is an incomplete replicator that in order to replicate, must infect a host cell, use the host cell's DNA mechanisms to complement its own genetics in order to replicate, and in the process, kills the host cell? And if the host cell is a germ cell, the germ cell is dead, and you don't get any birth defects in a dead cell. Infant koalas aren't getting any birth defects, they are dying long before that, threatening the population with extinction.

Kleinman:

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Then, why are koalas threatened with extinction because of their retroviral infection?

Taq:

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They are threatened with extinction because of the EXOGENOUS retrovirus, not the endogenous retrovirus. The retrovirus is currently being spread like any other virus.

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You really aren't thinking clearly. For your story to work, an endogenous retrovirus must start out as an exogenous retrovirus that kills its host cell in order for the virus to survive and replicate. And if the host cell is a germ cell, the germ cell does not survive to differentiate and produce an adult. And now you want to claim that 203,000 exogenous retroviruses infect a germ cell lineage, but they don't do it to replicate and ultimately kill the germ cell, they incorporate into the host genome. You have given a very poor explanation of what these genetic sequences are being seen in the human and chimpanzee genomes. As a virologist, you should understand what a virus does to a host cell but instead, you make this totally illogical argument.

Kleinman:

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And if the host cell is a germ cell, the germ cell is dead, and you don't get any birth defects in a dead cell. Infant koalas aren't getting any birth defects, they are dying long before that, threatening the population with extinction.

Taq:

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Koalas are born with the ERVs from a currently active exogenous retrovirus. This is a fact. Deny it all you want, that fact still exists.

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You sound like the layman ringo when you say "This is a fact." What is a fact is that the survival of a germ cell with a single retroviral infection is questionable. And you claim a germ cell line can survive 203,000 retroviral infections and the germ cell line does just fine. Stick with laymen like ringo when you make claims like that.

Kleinman:

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For your story to work, an endogenous retrovirus must start out as an exogenous retrovirus that kills its host cell in order for the virus to survive and replicate. And if the host cell is a germ cell, the germ cell does not survive to differentiate and produce an adult.

Taq:

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Koalas are born with the ERVs from a currently circulating exogenous retrovirus. Obviously, the germ cells with these insertions are functioning just fine, as is embryonic development. You are wrong.

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ringo might believe your claim because he doesn't understand how viruses replicate and then kill their host cell. Exogenous retroviruses have to infect the germ cell, not just currently circulating in Koalas that are born, because they are just in somatic cells, not germ cells. This is a fact.

Kleinman:

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You sound like the layman ringo when you say "This is a fact."

Taq:

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It is a fact that ERV's from KoRV insertions (an active exogenous retrovirus) are being vertically inherited in koalas.

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Viruses can be incorporated into the host genome in some cells. Anyone that has chicken pox and then gets shingles will know that. These incorporated viruses can reactivate and still cause disease. This explains why HIV cannot be cured and if HIV patients stop treatment, they relapse. You can't explain how a germ cell line gets 203,000 retroviral infections but the lineage does just fine, however, you present an example where koalas get a single retroviral infection and it may drive koalas extinct. You don't know, and you see what you want to see. That is not the scientific method.How does a germ cell line get 203,000 retroviral infections? The germ cell line must have receptors on the surface of the cell that the virus can bind to and enter the cell. And the virus does not replicate itself, it just enters the genome. No viral replication, and no host cell death, and it has to happen 203,000 times according to your claim. I think you and the research you are quoting are mistaking host genetic sequences that control the transcription of DNA with viral DNA. Superficially the sequences may appear the same but the belief that our germ cell line has been infected 203,000 times by retroviruses ignores the fact of what these viruses do to their host. The retrovirus that is infecting koalas could certainly be incorporated into the koalas' genome but it is also killing them. You are being illogical when you claim that it can happen 203,000 times without driving the lineage to extinction. These viruses survive by killing their host cells, this is a fact.

Kleinman:

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How does a germ cell line get 203,000 retroviral infections?

Taq:

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The same way it is happening in koalas.

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The same way that the koala population may go extinct? This is a fact.

Kleinman:

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I think you and the research you are quoting are mistaking host genetic sequences that control the transcription of DNA with viral DNA.

Taq:

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Baloney. These are viral insertions in the koala genome, and they match the currently active exogenous retrovirus. More importantly, there are pockets of koalas that have not been exposed to the virus and they lack these insertions in their genome. These insertions are also found in the genomes of germline cells, and they are passed on vertically as I already showed.

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Why would you claim that koalas don't have their own DNA that controls transcription? And just because a single viral genome can be inserted into the host genome you can conclude that 203,000 viral genomes can be inserted. These viruses survive by killing their host cells. This is a fact. Why won't you accept the fact that koalas are threatened by extinction from this virus, regardless of whether the insertion of the viral genome or not? And now you claim it happens 203,000 times. You are illogical.

Kleinman:

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Superficially the sequences may appear the same but the belief that our germ cell line has been infected 203,000 times by retroviruses ignores the fact of what these viruses do to their host.

Taq:

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You are the only one ignoring evidence here. There is evidence that there are insertions into the koala genome from a currently active exogenous retrovirus. These are found in the germline cells. The insertions are vertically inherited. There are even koala populations that do not have these insertions which demonstrates they were not a part of the host genome before the retrovirus began infecting koala populations.

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I'm not ignoring anything. Retroviruses survive by killing the host cell they infect but you refuse to accept this fact. And then you claim that 203,000 retroviruses can infect a germ cell line without killing that lineage just because a virus that is driving a koala population toward extinction is being inserted into the genome. You make no sense, just like you have never made sense of descent with modification.

Kleinman:

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You are being illogical when you claim that it can happen 203,000 times without driving the lineage to extinction.

Taq:

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The only one being illogical is you. You are the one ignoring mountains of evidence demonstrating an ongoing retroviral germline invasion of a mammalian genome.

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You fail to recognize one little fact. A single retroviral infection can drive a population to extinction, your own reference acknowledges this and HIV kills people with this disease if untreated. This is a fact. You surprise me with your illogic considering you claim to be a virologist. You claim a lineage can get 203,000 retroviral infections and the lineage does fine when empirical evidence shows that a single retroviral infection can kill that lineage. You see only what you want to see which is not the scientific method. You revealed the same kind of logic when we discussed recombination. You want to extrapolate the results of the Desai and Peabody experiments to all examples of evolution even though these experiments are done in controlled environments. Just because a virus can be inserted one time into a genome, you want to claim it can be done 203,000 times without doing harm to that lineage. You need to think more clearly about the claims you are making.