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Author Topic:   Exposing the evolution theory. Part 2
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 811 of 1104 (909326)
03-31-2023 5:17 PM
Reply to: Message 809 by Kleinman
03-31-2023 5:13 PM


Kleinman writes:
So you are both an atheist and agnostic.
Yes.
Most people are more interested in what we believe, not in what we can know. In fact, there are agnostic Christians who believe in God. That's why I usually refer to myself as an atheist.

This message is a reply to:
 Message 809 by Kleinman, posted 03-31-2023 5:13 PM Kleinman has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 812 of 1104 (909327)
03-31-2023 5:22 PM
Reply to: Message 804 by Kleinman
03-31-2023 4:22 PM


Kleinman writes:
None of these papers explain how drug resistance evolves.
What a fucking moron. This is why people see no need to respond to your posts on this subject. Even when shown exactly what you are asking for you deny what is right in front of you.

This message is a reply to:
 Message 804 by Kleinman, posted 03-31-2023 4:22 PM Kleinman has replied

Replies to this message:
 Message 814 by Kleinman, posted 03-31-2023 6:20 PM Taq has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 813 of 1104 (909329)
03-31-2023 6:18 PM
Reply to: Message 810 by Taq
03-31-2023 5:15 PM


Re: problems with detecting design
Kleinman:
Do you have any scientific proof for such a belief, that is all vertebrate DNA sequences that have similarities to viral sequences came from viruses?
Taq:
"We used the PCR to screen for the presence of endogenous retroviruses within the genomes of 18 vertebrate orders across eight classes, concentrating on reptilian, amphibian, and piscine hosts. Thirty novel retroviral sequences were isolated and characterized by sequencing approximately 1 kb of their encoded protease and reverse transcriptase genes. Isolation of novel viruses from so many disparate hosts suggests that retroviruses are likely to be ubiquitous within all but the most basal vertebrate classes and, furthermore, gives a good indication of the overall retroviral diversity within vertebrates. "
Retroviral Diversity and Distribution in Vertebrates - PMC

Did they identify 203,000 retroviruses in these genomes?
Kleinman:
Is the virus causing the host cell to produce viral components rather than the host cell doing its own metabolic processes?
Taq:
First of all, a cell can do both at the same time.

Second, there are mechanisms that shut down transcription of viral DNA.

"TRIM28 is a corepressor that mediates transcriptional silencing by establishing local heterochromatin. Here, we show that deletion of TRIM28 in neural progenitor cells (NPCs) results in high-level expression of two groups of endogenous retroviruses (ERVs): IAP1 and MMERVK10C. We find that NPCs use TRIM28-mediated histone modifications to dynamically regulate transcription and silencing of ERVs, which is in contrast to other somatic cell types using DNA methylation. We also show that derepression of ERVs influences transcriptional dynamics in NPCs through the activation of nearby genes and the expression of long noncoding RNAs. These findings demonstrate a unique dynamic transcriptional regulation of ERVs in NPCs. Our results warrant future studies on the role of ERVs in the healthy and diseased brain."
TRIM28 represses transcription of endogenous retroviruses in neural progenitor cells - PubMed

What happens if a germ cell has more than one retrovirus active in the cell at a time?
Kleinman:
Of the 203,000 ERVs you claim that humans have, how many DNA sequences of viral proteins have been identified?
Taq:
As stated multiple times already, 90% are solo LTR's that don't have any protein coding regions. About 10% have remnants of genes for proteins.

Is your claim that the LTRs remain but the protein-coding region has disappeared? Do the LTRs ever get a mutation when they are replicated?
Kleinman:
Are the only DNA repeats seen in vertebrates due to ERVs?
Taq:
There are many different types of DNA repeats, retroviral LTR's being one of those types.

Are all LTRs associated with retroviruses?
Kleinman:
Are you claiming that the protein-coding portion of viral insertions can get mutations and other forms of genetic transformations but DNA repeats remain constant and never change?
Taq:
The repeats evolve as well. However (for the upteenth time), it is common for homologous recombination to occur between the LTR's because they have identical sequence. This loops out the protein coding genes so that all you are left with is a single LTR.

If you don't have the viral protein-coding genes in the genetic sequence, and the LTRs have evolved, how can you be sure this genetic sequence is from a retrovirus?
Kleinman:
By the way, the truck is decomposing as well as the tires are missing.
Taq:
Just as ERVs take on substitutions, deletions, insertions, and near complete removal by homologous recombination.

How do you determine that this piece of genetic material is the remnant of a retrovirus rather than host DNA when the viral protein-coding DNA is gone? Can the host vertebrate genome have its own LTRs that are not from a virus?
Kleinman:
Do DNA repeats only occur with viral insertions?
Taq:
DNA repeats do occur outside of viral insertions, but the sequence is different. Retroviral LTRs are recognized by their sequence.

Can vertebrates have retrotransposons not associated with retroviruses?

This message is a reply to:
 Message 810 by Taq, posted 03-31-2023 5:15 PM Taq has replied

Replies to this message:
 Message 823 by Taq, posted 04-03-2023 6:52 PM Kleinman has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 814 of 1104 (909330)
03-31-2023 6:20 PM
Reply to: Message 812 by Taq
03-31-2023 5:22 PM


Kleinman:
None of these papers explain how drug resistance evolves.
Taq:
What a fucking moron. This is why people see no need to respond to your posts on this subject. Even when shown exactly what you are asking for you deny what is right in front of you.

It appears you are having difficulty posting a quote from any of your papers that you think describes the mathematics of the evolution of drug resistance. The fact is that biologists have failed to describe the physics and mathematics of biological evolution and the evolution of drug resistance. I'm familiar with most of those papers you listed and none give the correct mathematics. None of these papers explain why it takes a billion replications for each adaptive mutation in the Kishony and Lenski experiments. You are wrong Taq and you are angry because you know it.

This message is a reply to:
 Message 812 by Taq, posted 03-31-2023 5:22 PM Taq has replied

Replies to this message:
 Message 825 by Taq, posted 04-03-2023 7:01 PM Kleinman has replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 815 of 1104 (909331)
03-31-2023 6:27 PM
Reply to: Message 800 by Taq
03-31-2023 3:34 PM


Message 800
quote:
Card KJ, Thomas MD, Graves JL Jr, Barrick JE, Lenski RE. Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A. 2021 Feb 2;118(5):e2016886118. doi: 10.1073/pnas.2016886118. PMID: 33441451; PMCID: PMC7865137.

Lenski RE. Bacterial evolution and the cost of antibiotic resistance. Int Microbiol. 1998 Dec;1(4):265-70. PMID: 10943373.

Article Source: Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection
Card KJ, LaBar T, Gomez JB, Lenski RE (2019) Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection. PLOS Biology 17(10): e3000397. Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection | PLOS Biology

Stracy M, Snitser O, Yelin I, Amer Y, Parizade M, Katz R, Rimler G, Wolf T, Herzel E, Koren G, Kuint J, Foxman B, Chodick G, Shalev V, Kishony R. Minimizing treatment-induced emergence of antibiotic resistance in bacterial infections. Science. 2022 Feb 25;375(6583):889-894. doi: 10.1126/science.abg9868. Epub 2022 Feb 24. PMID: 35201862; PMCID: PMC7612469.

Baym M, Lieberman TD, Kelsic ED, Chait R, Gross R, Yelin I, Kishony R. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016 Sep 9;353(6304):1147-51. doi: 10.1126/science.aag0822. PMID: 27609891; PMCID: PMC5534434.i
Happy Alert: These 5 listed papers are actual science showing genomic evolution of antibiotic resistance, something Kleinman claims doesn't exist. Unlike Kleinman's sloppy and errant works these papers are reviewed, accepted and represent the actual facts of the processes.
Kleinman writes:

None of these papers explain how drug resistance evolves.

Taq responds:
What a fucking moron. This is why people see no need to respond to your posts on this subject. Even when shown exactly what you are asking for you deny what is right in front of you.
This discussion has left any science topic behind and is now nothing more than an intransigent Kleinman pushing a religious agenda.

Stop Tzar Vladimir the Condemned!

This message is a reply to:
 Message 800 by Taq, posted 03-31-2023 3:34 PM Taq has not replied

Replies to this message:
 Message 816 by Kleinman, posted 03-31-2023 6:58 PM AZPaul3 has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 816 of 1104 (909333)
03-31-2023 6:58 PM
Reply to: Message 815 by AZPaul3
03-31-2023 6:27 PM


AZPaul3:
This discussion has left any science topic behind and is now nothing more than an intransigent Kleinman pushing a religious agenda.
None of Taq's references explain how drug resistance occurs and why it takes a billion replications for each adaptive mutation for a single selection pressure in the Kishony and Lenski experiments. I realize it is difficult for you and biologists to understand the mathematics of evolution but here it is.
For a single selection pressure:
The basic science and mathematics of random mutation and natural selection
And for multiple simultaneous selection pressures:
The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance
And here is the correct probability equation for a single adaptive step in a single selection pressure environment:
P(X) = (1-(1-P(Beneficial)μ)^N
where P(X) is the probability of the beneficial mutation occurring, P(Beneficial) is the probability that of all the mutations that may occur at that site that it is the beneficial mutation, μ is the mutation rate, and N it the number of replications that the particular variant does.
I don't post this for you AZPaul because you refuse to learn about probability theory and the "at least one" rule. This is for any of those that know a little about probability theory. That is how you do the mathematics of descent with modification and adaptation, a stochastic process.

This message is a reply to:
 Message 815 by AZPaul3, posted 03-31-2023 6:27 PM AZPaul3 has replied

Replies to this message:
 Message 817 by AZPaul3, posted 03-31-2023 7:31 PM Kleinman has replied
 Message 822 by Taq, posted 04-03-2023 6:47 PM Kleinman has replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(1)
Message 817 of 1104 (909334)
03-31-2023 7:31 PM
Reply to: Message 816 by Kleinman
03-31-2023 6:58 PM


An intransigent Kleinman pushing a religious agenda.

Stop Tzar Vladimir the Condemned!

This message is a reply to:
 Message 816 by Kleinman, posted 03-31-2023 6:58 PM Kleinman has replied

Replies to this message:
 Message 818 by Kleinman, posted 03-31-2023 7:41 PM AZPaul3 has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 818 of 1104 (909335)
03-31-2023 7:41 PM
Reply to: Message 817 by AZPaul3
03-31-2023 7:31 PM


AZPaul3:
An intransigent Kleinman pushing a religious agenda.
You are confuse AZPaul3, these papers explain how drug resistance evolves.
For a single selection pressure:
The basic science and mathematics of random mutation and natural selection
And for multiple simultaneous selection pressures:
The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance
This math fits the experimental and empirical data of biological evolutionary descent with modification and adaptation. It explains why it takes a billion replications for each adaptive mutation in the Kishony and Lenski biological evolutionary experiments. You won't accept this mathematical and physical fact of life because it doesn't fit your belief system.

This message is a reply to:
 Message 817 by AZPaul3, posted 03-31-2023 7:31 PM AZPaul3 has replied

Replies to this message:
 Message 819 by AZPaul3, posted 03-31-2023 8:05 PM Kleinman has replied

  
AZPaul3
Member
Posts: 8513
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.3


(2)
Message 819 of 1104 (909336)
03-31-2023 8:05 PM
Reply to: Message 818 by Kleinman
03-31-2023 7:41 PM


Bogus.
An intransigent Kleinman pushing his religious agenda.

Stop Tzar Vladimir the Condemned!

This message is a reply to:
 Message 818 by Kleinman, posted 03-31-2023 7:41 PM Kleinman has replied

Replies to this message:
 Message 821 by Kleinman, posted 04-03-2023 9:17 AM AZPaul3 has not replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 820 of 1104 (909351)
04-01-2023 11:17 AM


It is worth summarizing this discussion on ERVs since Taq has been playing an ongoing April Fool joke on everyone.
The reader should recall that Taq is using the existence of ERVs in humans and chimpanzees as proof that the two species are related. In Message 772 we had the following exchange:
Kleinman:
203,000 retroviral infections to a germ cell line and the lineage does just fine is part of your belief system.
Taq:
It's an observed fact as detailed in the 2001 human genome paper.

A few posts later, Message 787, I asked Taq the following:
Kleinman:
Tell us what the genetic structure of a virus is, for example, HIV and tell us if multicellular replicators have any similar types of genetic structures.
Taq:
A generic retroviral genome looks like this:
Multicellular replicators have insertions of these retroviral genomes in their genome. They are easily recognizable as retroviral genomes and LTRs from retroviruses. The 4-6 bases of host DNA at either end of the viral genome for full length insertions is also a dead give away because those are created during insertion of the retroviral genome.

Taq has said something different from his initial claim. He now says, "They are easily recognizable as retroviral genomes and LTRs from retroviruses." He is now shifting his argument from ERVs to LTRs. Note that his figure shows that an exogenous retrovirus has a gag, pol, and env region where the genome is coding for proteins unique to the virus. For those not familiar with what an LTR is, you can read the following Wikipedia link where you can find a discussion on Repeated Sequence DNA:
Repeated sequence (DNA) - Wikipedia(DNA)
Interspersed repeats
Interspersed repeats are identical or similar DNA sequences which are found in different locations throughout the genome. Interspersed repeats are distinguished from tandem repeats in that the repeated sequences are not directly adjacent to each other but instead may be scattered among different chromosomes or far apart on the same chromosome. Most interspersed repeats are transposable elements (TEs), mobile sequences which can be “cut and pasted” or “copied and pasted” into different places in the genome. TEs were originally called “jumping genes” for their ability to move, yet this term is somewhat misleading as not all TEs are discrete genes.
and slightly further down in this link:
Long-terminal repeat retrotransposons (LTRs) are a third major class of retrotransposons and are characterized by highly repetitive sequences as the ends of the repeat.
Taq's argument has made a shift from talking about ERVs now to talking about LTRs. Then in Message 794, I asked Taq the following and he gave this response:
Kleinman:
You haven't fully answered the question, do multicellular replicators have any genetic structures like viruses?
Taq:
Vertebrates do have DNA sequences in their genome that are like viruses because they came from viruses.

Here is a short discussion of Repeated sequence (DNA):
Repeated sequence (DNA) - Wikipedia(DNA)
Repeated sequences (also known as repetitive elements, repeating units or repeats) are short or long patterns of nucleic acids (DNA or RNA) that occur in multiple copies throughout the genome. In many organisms, a significant fraction of the genomic DNA is repetitive, with over two-thirds of the sequence consisting of repetitive elements in humans. Some of these repeated sequences are necessary for maintaining important genome structures such as telomeres or centromeres.
And further done in that post, I asked the following:
Kleinman:
And have the unique viral proteins been identified in the claimed 203,000 viral infections you claim our ancestors have had and been passed to us?
Taq:
About 90% of human ERV's are solo LTR's due to homologous recombination, as mentioned earlier. Again, these LTR's are specific to viruses, and we know where they come from. The other 10% still have parts of the coding regions from the original provirus.

Miraculously, 90% of the ERVs have lost their protein coding regions and only LTRs remain and the other 10% have only parts remaining, no intact viral genomes in that 203,000 ERVs that relate humans and chimpanzees. But Taq says that he is absolutely sure these LTRs are from retroviruses and he gives his proof in Message 802:
Taq:
There's little doubt that this is a truck. In the same way, there is little doubt that we are looking at insertions from retroviruses even if a few of the parts are missing. In case you aren't aware, DNA deletions happen. It's a normal type of occurrence. Homologous recombination is also a very natural process that will delete everything in the protein-coding regions and only leave one LTR.
The correct picture he should use for his argument looks like this:
Taq can look at this picture and tell us what vehicle these tires came off simply by the brand of tire. If the tire name is Goodyear, it came from a Ford, and if the tire name says Bridgestone, it came from a Dodge, and if the tire brand says Michelin, obviously that came from a Mercedes.
It is no surprise that Taq would rather argue about what he thinks atheism and agnosticism mean, or post a bunch of references that he claims explain how drug resistance evolves and then gets angry because I point out that he doesn't quote from any of them.
What Taq calls evidence is his biased interpretation of his observations. He may think that humans and chimpanzees are related but he does this based on his incorrect understanding of the physics and mathematics of biological evolution.

Replies to this message:
 Message 824 by Taq, posted 04-03-2023 6:56 PM Kleinman has replied

  
Kleinman
Member (Idle past 335 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 821 of 1104 (909405)
04-03-2023 9:17 AM
Reply to: Message 819 by AZPaul3
03-31-2023 8:05 PM


AZPaul3:
Bogus.

An intransigent Kleinman pushing his religious agenda.
The following two papers that give the mathematics for descent with modification (and adaptation) are what AZPaul3 is calling bogus.
For a single selection pressure:
The basic science and mathematics of random mutation and natural selection
And for multiple simultaneous selection pressures:
The mathematics of random mutation and natural selection for multiple simultaneous selection pressures and the evolution of antimicrobial drug resistance
He seems to think that the peer reviewers at Statistics in Medicine did an inadequate job peer reviewing these papers. The following video explains what is happening in scientific publishing:
https://www.youtube.com/watch?v=5-K3obvnKYQ&ab_channel=Bu...
Here is the website where they are monitoring retracted papers:
Retraction Watch – Tracking retractions as a window into the scientific process
Here is AZPaul3's big chance to get these "bogus" papers pulled. Is AZPaul3 all talk and no action?

This message is a reply to:
 Message 819 by AZPaul3, posted 03-31-2023 8:05 PM AZPaul3 has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 822 of 1104 (909419)
04-03-2023 6:47 PM
Reply to: Message 816 by Kleinman
03-31-2023 6:58 PM


Kleinman writes:
None of Taq's references explain how drug resistance occurs and why it takes a billion replications for each adaptive mutation for a single selection pressure in the Kishony and Lenski experiments.
All of them do. Read the papers you fucking moron.

This message is a reply to:
 Message 816 by Kleinman, posted 03-31-2023 6:58 PM Kleinman has replied

Replies to this message:
 Message 827 by Kleinman, posted 04-03-2023 8:20 PM Taq has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 823 of 1104 (909421)
04-03-2023 6:52 PM
Reply to: Message 813 by Kleinman
03-31-2023 6:18 PM


Re: problems with detecting design
Kleinman writes:
Did they identify 203,000 retroviruses in these genomes?
They weren't only trying to detect the presence of ERV's, and they were widespread amongst vertebrates.
What happens if a germ cell has more than one retrovirus active in the cell at a time?
Apparently, nothing. There are koalas with over 50 recently inserted ERVs and they are having offspring without a hitch.
Is your claim that the LTRs remain but the protein-coding region has disappeared? Do the LTRs ever get a mutation when they are replicated?
Already answered multiple times.
Are all LTRs associated with retroviruses?
LTRs are by definition from retroviral insertions.
If you don't have the viral protein-coding genes in the genetic sequence, and the LTRs have evolved, how can you be sure this genetic sequence is from a retrovirus?
The same way you can identify a partial fingerprint.
How do you determine that this piece of genetic material is the remnant of a retrovirus rather than host DNA when the viral protein-coding DNA is gone?
The same way we know a partial fingerprint is from a finger.
Can the host vertebrate genome have its own LTRs that are not from a virus?
Can a murder weapon have its own fingerprints?
All you are trying to do is used the Omphalos argument. Arguing that the human genome was created with genetic scars from retroviral insertion is nonsense. It's like saying the universe was created last Thursday, complete with a false history and false memories.

This message is a reply to:
 Message 813 by Kleinman, posted 03-31-2023 6:18 PM Kleinman has replied

Replies to this message:
 Message 829 by Kleinman, posted 04-03-2023 8:26 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 824 of 1104 (909422)
04-03-2023 6:56 PM
Reply to: Message 820 by Kleinman
04-01-2023 11:17 AM


Kleinman writes:
He is now shifting his argument from ERVs to LTRs.
LTRs are ERVs, you fucking moron.
The correct picture he should use for his argument looks like this:
You would deny that those are tires. Instead, they are round pieces of rubber that were created with the Earth 6,000 years ago. They never came from a tire factory, nor did they ever reside on a car.
Taq can look at this picture and tell us what vehicle these tires came off simply by the brand of tire.
I can tell you they are tires. In the same way, LTRs are the tires of the ERV vehicle. Your argument seems to be that the Earth was created with those tires already in place.
It is no surprise that Taq would rather argue about what he thinks atheism and agnosticism mean, or post a bunch of references that he claims explain how drug resistance evolves and then gets angry because I point out that he doesn't quote from any of them.
You fucking moron. You don't even understand the papers you claim to reference. You don't even understand that modeling asexual reproduction does not accurately model the evolution of sexual species. You can't even understand that the mutation rate is different in humans and in bacteria.

This message is a reply to:
 Message 820 by Kleinman, posted 04-01-2023 11:17 AM Kleinman has replied

Replies to this message:
 Message 830 by Kleinman, posted 04-03-2023 8:30 PM Taq has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 825 of 1104 (909423)
04-03-2023 7:01 PM
Reply to: Message 814 by Kleinman
03-31-2023 6:20 PM


Kleinman writes:
It appears you are having difficulty posting a quote from any of your papers that you think describes the mathematics of the evolution of drug resistance.
You don't need mathematics to explain how antibiotic resistance evolves, you fucking moron.
The fact is that biologists have failed to describe the physics and mathematics of biological evolution and the evolution of drug resistance.
Prove it. Show me every paper in existence on antibiotic resistance and show me that none of them have the requisite math.
I'm familiar with most of those papers you listed and none give the correct mathematics.
You wouldn't recognize correct math if it was right in front of you, you fucking moron.

This message is a reply to:
 Message 814 by Kleinman, posted 03-31-2023 6:20 PM Kleinman has replied

Replies to this message:
 Message 831 by Kleinman, posted 04-03-2023 8:36 PM Taq has replied

  
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