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Author Topic:   Exposing the evolution theory. Part 2
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 796 of 1104 (909306)
03-31-2023 11:07 AM
Reply to: Message 791 by Kleinman
03-30-2023 7:05 PM


Kleinman writes:
Are you going to post a link to a thread in this forum where you explain how drug resistance evolves and why cancer treatments fail?
Sure. Here you go:
https://www.evcforum.net/dm.php?control=msg&t=20319
You might as well tell Kishony and Lenski how their experiments work since you have figured out how descent with modification and adaptation works.
They understand their own findings just fine.

This message is a reply to:
 Message 791 by Kleinman, posted 03-30-2023 7:05 PM Kleinman has replied

Replies to this message:
 Message 799 by Kleinman, posted 03-31-2023 11:53 AM Taq has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 797 of 1104 (909307)
03-31-2023 11:48 AM
Reply to: Message 794 by Taq
03-31-2023 11:04 AM


Re: problems with detecting design
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.

Are you claiming that all vertebrate DNA sequences that have similarities to viral sequences came from insertions of viruses?
Kleinman:
How about non-protein coding portions of the viral genome that take control of the host cell to reproduce more viruses rather than the host cell carrying on its own metabolic processes?
Taq:
The viral promoters are specific to viruses.

How do viruses cause vertebrate cells to initiate the transcription of viral proteins?
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.

Are you saying that the DNA sequences that code for the viral proteins have not been identified in their entirety, only fragments? How about in koalas infected by a retrovirus, have those DNA sequences been identified?
In your previous post, Message 787, you said the following:
Taq:
Guess what we see with ERVs? We see those host DNA repeats. That means ERVs are the result of viral integration.
Are the only DNA replications seen in vertebrates due to ERVs? Why are DNA repeats identifiable but the protein-coding portions of viral insertions are only seen in fragments?

This message is a reply to:
 Message 794 by Taq, posted 03-31-2023 11:04 AM Taq has replied

Replies to this message:
 Message 802 by Taq, posted 03-31-2023 3:45 PM Kleinman has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 798 of 1104 (909308)
03-31-2023 11:50 AM
Reply to: Message 795 by Taq
03-31-2023 11:05 AM


Kleinman:
So you don't know whether a deity exists or not.
Taq:
I don't believe any deities exist which makes me an atheist.

I also don't believe that Bigfoot exists. At the same time, I can't say with 100% certainty that Bigfoot doesn't exist, but I have yet to see any compelling evidence that Bigfoot does exist, so I don't believe that Bigfoot exists. The same with deities.

What percent certainty do you say that any deities don't exist? And what is your evidence for this claim?

This message is a reply to:
 Message 795 by Taq, posted 03-31-2023 11:05 AM Taq has replied

Replies to this message:
 Message 801 by Taq, posted 03-31-2023 3:35 PM Kleinman has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 799 of 1104 (909309)
03-31-2023 11:53 AM
Reply to: Message 796 by Taq
03-31-2023 11:07 AM


Kleinman:
Are you going to post a link to a thread in this forum where you explain how drug resistance evolves and why cancer treatments fail?
Taq:
Sure. Here you go:

https://www.evcforum.net/dm.php?control=msg&t=20319

And
Kleinman:
You might as well tell Kishony and Lenski how their experiments work since you have figured out how descent with modification and adaptation works.
Taq:
They understand their own findings just fine.

Neither you, Kishony, nor Lenski, have ever published how drug resistance evolves or why cancer treatments fail mathematically. Nor have you, Kishony and Lenski published or explained how their experiments work mathematically.

This message is a reply to:
 Message 796 by Taq, posted 03-31-2023 11:07 AM Taq has replied

Replies to this message:
 Message 800 by Taq, posted 03-31-2023 3:34 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(1)
Message 800 of 1104 (909312)
03-31-2023 3:34 PM
Reply to: Message 799 by Kleinman
03-31-2023 11:53 AM


Kleinman writes:
Neither you, Kishony, nor Lenski, have ever published how drug resistance evolves
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

This message is a reply to:
 Message 799 by Kleinman, posted 03-31-2023 11:53 AM Kleinman has replied

Replies to this message:
 Message 804 by Kleinman, posted 03-31-2023 4:22 PM Taq has replied
 Message 815 by AZPaul3, posted 03-31-2023 6:27 PM Taq has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 801 of 1104 (909313)
03-31-2023 3:35 PM
Reply to: Message 798 by Kleinman
03-31-2023 11:50 AM


Kleinman writes:
What percent certainty do you say that any deities don't exist?
Less than absolutely certain. There's no percentage involved.
And what is your evidence for this claim?
My claim for what I do or don't believe? I guess you will have to take my word for it.

This message is a reply to:
 Message 798 by Kleinman, posted 03-31-2023 11:50 AM Kleinman has replied

Replies to this message:
 Message 805 by Kleinman, posted 03-31-2023 4:23 PM Taq has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 802 of 1104 (909314)
03-31-2023 3:45 PM
Reply to: Message 797 by Kleinman
03-31-2023 11:48 AM


Re: problems with detecting design
Kleinman writes:
Are you claiming that all vertebrate DNA sequences that have similarities to viral sequences came from insertions of viruses?
Either directly or indirectly, yes. Viral sequences can still hop around through transposon activity without an active infection.
How do viruses cause vertebrate cells to initiate the transcription of viral proteins?
The LTR's bind transcription factors which drives transcription of the provirus.
Are you saying that the DNA sequences that code for the viral proteins have not been identified in their entirety, only fragments?
Depends on the ERV. Different ERV's have retained different amounts of sequence as they have evolved in the host genome. Across the many HERV-K insertions there is enough sequence between them that a functional retrovirus can be reconstructed from their consensus sequence.
Are the only DNA replications seen in vertebrates due to ERVs?
The entire genome is replicated, last I checked.
Why are DNA repeats identifiable but the protein-coding portions of viral insertions are only seen in fragments?
For the same reason that we can't identify the type of tires on this truck.
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.

This message is a reply to:
 Message 797 by Kleinman, posted 03-31-2023 11:48 AM Kleinman has replied

Replies to this message:
 Message 806 by Kleinman, posted 03-31-2023 4:33 PM Taq has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 803 of 1104 (909315)
03-31-2023 3:48 PM
Reply to: Message 793 by Kleinman
03-31-2023 9:35 AM


Kleinman writes:
Atheists seem to think that they know. Do you want to tell us what evidence they have to make their assertion?
When you have to start putting words in other peoples' mouths, perhaps you should take a step back and rethink your argument.
Atheists are telling you that they can't be absolutely certain that deities exist. They are atheists because they don't believe deities exist. That's our position.

This message is a reply to:
 Message 793 by Kleinman, posted 03-31-2023 9:35 AM Kleinman has replied

Replies to this message:
 Message 807 by Kleinman, posted 03-31-2023 4:34 PM Taq has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 804 of 1104 (909317)
03-31-2023 4:22 PM
Reply to: Message 800 by Taq
03-31-2023 3:34 PM


Kleinman:
Neither you, Kishony, nor Lenski, have ever published how drug resistance evolves
Taq:
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

None of these papers explain how drug resistance evolves. That's why you don't quote from these papers.

This message is a reply to:
 Message 800 by Taq, posted 03-31-2023 3:34 PM Taq has replied

Replies to this message:
 Message 812 by Taq, posted 03-31-2023 5:22 PM Kleinman has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 805 of 1104 (909318)
03-31-2023 4:23 PM
Reply to: Message 801 by Taq
03-31-2023 3:35 PM


Kleinman:
What percent certainty do you say that any deities don't exist?
Taq:
Less than absolutely certain. There's no percentage involved.

And
Kleinman:
And what is your evidence for this claim?
Taq:
My claim for what I do or don't believe? I guess you will have to take my word for it.

Sure, it is your religious belief.

This message is a reply to:
 Message 801 by Taq, posted 03-31-2023 3:35 PM Taq has not replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 806 of 1104 (909319)
03-31-2023 4:33 PM
Reply to: Message 802 by Taq
03-31-2023 3:45 PM


Re: problems with detecting design
Kleinman:
Are you claiming that all vertebrate DNA sequences that have similarities to viral sequences came from insertions of viruses?
Taq:
Either directly or indirectly, yes. Viral sequences can still hop around through transposon activity without an active infection.

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?
Kleinman:
How do viruses cause vertebrate cells to initiate the transcription of viral proteins?
Taq:
The LTR's bind transcription factors which drives transcription of the provirus.

Is the virus causing the host cell to produce viral components rather than the host cell doing its own metabolic processes?
Kleinman:
Are you saying that the DNA sequences that code for the viral proteins have not been identified in their entirety, only fragments?
Taq:
Depends on the ERV. Different ERV's have retained different amounts of sequence as they have evolved in the host genome. Across the many HERV-K insertions there is enough sequence between them that a functional retrovirus can be reconstructed from their consensus sequence.

Of the 203,000 ERVs you claim that humans have, how many DNA sequences of viral proteins have been identified?
Kleinman:
Are the only DNA replications seen in vertebrates due to ERVs?
Taq:
The entire genome is replicated, last I checked.

That's not the question. I'll rephrase it. Are the only DNA repeats seen in vertebrates due to ERVs?
Kleinman:
Why are DNA repeats identifiable but the protein-coding portions of viral insertions are only seen in fragments?
Taq:
For the same reason that we can't identify the type of tires on this truck.

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.

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? And if so, why? By the way, the truck is decomposing as well as the tires are missing.
And I ask you again. Do DNA repeats only occur with viral insertions? Do vertebrate genomes have DNA repeats not associated with viral insertions?

This message is a reply to:
 Message 802 by Taq, posted 03-31-2023 3:45 PM Taq has replied

Replies to this message:
 Message 810 by Taq, posted 03-31-2023 5:15 PM Kleinman has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 807 of 1104 (909320)
03-31-2023 4:34 PM
Reply to: Message 803 by Taq
03-31-2023 3:48 PM


Kleinman:
Atheists seem to think that they know. Do you want to tell us what evidence they have to make their assertion?
Taq:
When you have to start putting words in other peoples' mouths, perhaps you should take a step back and rethink your argument.

Atheists are telling you that they can't be absolutely certain that deities exist. They are atheists because they don't believe deities exist. That's our position.

Go ahead and be as illogical as you want. If you want to say you are an atheist that doesn't know whether deities exist or not, that is fine. However, some might say that you are confusing the meaning of "atheist" and "agnostic".

This message is a reply to:
 Message 803 by Taq, posted 03-31-2023 3:48 PM Taq has replied

Replies to this message:
 Message 808 by Taq, posted 03-31-2023 5:05 PM Kleinman has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 808 of 1104 (909322)
03-31-2023 5:05 PM
Reply to: Message 807 by Kleinman
03-31-2023 4:34 PM


Kleinman writes:
If you want to say you are an atheist that doesn't know whether deities exist or not, that is fine.
Atheism is about what you believe, not what you know.
quote:
Agnostic isn’t just a “weaker” version of being an atheist. It answers a different question. Atheism is about what you believe. Agnosticism is about what you know.
What is Atheism? - American Atheists
A- = without
-theism = belief in deities
Atheism = without a belief in deities
However, some might say that you are confusing the meaning of "atheist" and "agnostic".
They might say that, and they would be wrong.

This message is a reply to:
 Message 807 by Kleinman, posted 03-31-2023 4:34 PM Kleinman has replied

Replies to this message:
 Message 809 by Kleinman, posted 03-31-2023 5:13 PM Taq has replied

  
Kleinman
Member (Idle past 334 days)
Posts: 2142
From: United States
Joined: 10-06-2016


Message 809 of 1104 (909324)
03-31-2023 5:13 PM
Reply to: Message 808 by Taq
03-31-2023 5:05 PM


Kleinman writes:
If you want to say you are an atheist that doesn't know whether deities exist or not, that is fine.
Atheism is about what you believe, not what you know.
quote:
Agnostic isn’t just a “weaker” version of being an atheist. It answers a different question. Atheism is about what you believe. Agnosticism is about what you know.
What is Atheism? - American Atheists
A- = without
-theism = belief in deities
Atheism = without a belief in deities
However, some might say that you are confusing the meaning of "atheist" and "agnostic".
They might say that, and they would be wrong.
So you are both an atheist and agnostic. But you still haven't told us whether a vertebrate cell can have DNA repeats not associated with a viral insertion.

This message is a reply to:
 Message 808 by Taq, posted 03-31-2023 5:05 PM Taq has replied

Replies to this message:
 Message 811 by Taq, posted 03-31-2023 5:17 PM Kleinman has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 810 of 1104 (909325)
03-31-2023 5:15 PM
Reply to: Message 806 by Kleinman
03-31-2023 4:33 PM


Re: problems with detecting design
Kleinman writes:
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?
"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
Is the virus causing the host cell to produce viral components rather than the host cell doing its own metabolic processes?
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
Of the 203,000 ERVs you claim that humans have, how many DNA sequences of viral proteins have been identified?
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.
Are the only DNA repeats seen in vertebrates due to ERVs?
There are many different types of DNA repeats, retroviral LTR's being one of those types.
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?
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.
By the way, the truck is decomposing as well as the tires are missing.
Just as ERVs take on substitutions, deletions, insertions, and near complete removal by homologous recombination.
Do DNA repeats only occur with viral insertions?
DNA repeats do occur outside of viral insertions, but the sequence is different. Retroviral LTRs are recognized by their sequence.

This message is a reply to:
 Message 806 by Kleinman, posted 03-31-2023 4:33 PM Kleinman has replied

Replies to this message:
 Message 813 by Kleinman, posted 03-31-2023 6:18 PM Taq has replied

  
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