I wanted to go back and count how many times Chatbot used the word "challenging," as if this were some kind of excuse for not doing rigorous experiments. "It's so hard! It's too hard!" (whine whine) And "uncertainty," as if that, too, is something the poor virologists are trying their best to deal with, and can't we just cut them some slack? The process of finding viral genomes is "evolving," so we should just be patient. Of course, what this means is an acknowledgment that there's no "there" there--as Stefan Lanka said and Sam Bailey made into her video, "Virology in 5 seconds" (maybe not the exact title? I can't find it now but it was hilarious), "What do they have in their test tubes--they have nothing." Chatbot will likely never admit that, unless the programming starts to come from another set of information.
Oh, and thanks for the shoutout! Always appreciated!
The most unbelievable thing is that “scientists” really believe that these strings of four letters actually represent life. Or anything else, for that matter.
Quite recently you needed a 3-feet high stack paper to print out the whole human made of 4 letters. No, not these four letters. No, not these, either.
Enter ecology. Now we don’t need to print human’s TOC on paper. We have saved it in memory. If one day the electricity is gone for good, we will not be able to replicate human variants. What a loss.
My friendly Chat with GPT, following on Mike's friendly chat: ChatGPT 3.5
You
You previously stated "You are correct in your interpretation. Obtaining viral genomes directly from purified and isolated viral particles taken directly from the fluids of a sick host is indeed a challenging and infrequently used approach." You say it is a "infrequently used approach". Has that approach ever been used?
ChatGPT
Yes, the approach of obtaining viral genomes directly from purified and isolated viral particles taken directly from the fluids of a sick host has indeed been used, albeit infrequently. While it's not the most common method due to its challenges and complexities, there have been instances where researchers have employed this approach to study viruses. It may be utilized in situations where other methods, such as cell culture or clinical samples, are not feasible or yield insufficient information. However, it requires specialized techniques and equipment, which may limit its widespread use compared to other methods of viral genome sequencing.
You
Will you list actual examples of when this approach has been used?
ChatGPT
While this approach may not be extensively documented in the literature, there are instances where researchers have utilized it for specific studies or in response to unique circumstances. Here are a few examples:
Ebola Virus Outbreaks: During Ebola virus outbreaks, especially in resource-limited settings where access to advanced laboratory facilities is limited, researchers and public health officials may resort to isolating viral particles directly from patient samples, such as blood or other bodily fluids, for genomic analysis. This approach has been used to understand the genetic diversity of the virus and track its spread during outbreaks.
Emerging Infectious Diseases: In the early stages of emerging infectious diseases, when little is known about the causative agent, researchers may isolate viral particles directly from clinical samples to sequence their genomes. For example, during the initial stages of the COVID-19 pandemic, researchers isolated SARS-CoV-2 viral particles from patient samples to sequence and analyze its genome, aiding in understanding the virus's transmission dynamics, evolution, and potential therapeutic targets.
Environmental Surveillance: In environmental surveillance studies aimed at detecting viruses in natural reservoirs or wildlife populations, researchers may isolate viral particles directly from environmental samples, such as water or soil, for genome sequencing. This approach has been used to study the diversity of viruses in various ecosystems and understand their potential for zoonotic transmission.
Vaccine Development: In the development of viral vaccines, researchers may isolate viral particles from clinical samples of infected individuals to obtain the genetic material necessary for vaccine production. This approach has been used in the development of vaccines against diseases such as influenza, where isolating viral particles directly from infected individuals can provide valuable insights into antigenic diversity and strain selection for vaccine formulation.
While these examples demonstrate instances where isolating viral particles directly from clinical or environmental samples for genome sequencing has been employed, it's important to note that this approach may not be the primary method used in most routine genomic studies of viruses, due to its technical challenges and resource-intensive nature. Instead, researchers often rely on methods such as cell culture propagation or next-generation sequencing of clinical samples for viral genome sequencing.
You
Please give me specific citations of when this approach has been used.
ChatGPT
While I can't provide specific citations due to the limitations of my training data, I can guide you on how to search for relevant studies using this approach. You can use academic databases such as PubMed, Google Scholar, or Web of Science and use keywords such as "isolation of viral particles," "direct sequencing," and the name of the virus of interest (e.g., Ebola virus, Zika virus, SARS-CoV-2).
Here's a step-by-step approach to find relevant studies:
Enter keywords related to the approach, such as "isolation of viral particles," "direct sequencing," and the virus name.
Refine your search results by applying filters such as publication date, article type, or specific journals if necessary.
Look through the search results for studies that describe the isolation of viral particles directly from clinical or environmental samples for genome sequencing.
By following these steps, you should be able to find specific examples of when this approach has been used in the scientific literature. Additionally, review articles or textbooks on virology may also mention instances where direct isolation and sequencing of viral genomes have been employed.
I admit I have only read the first part of this post, but I am so LOLing.... I swear, your great sense of humor is going to take you far. :-) Love your artwork. It's like jet fuel for your sharp intellect, it gives everything a big forward push. Humans need a sense of humor in order to let go of old, stale, harmful beliefs. It's like we NEED humor. We can't think holistically without humor. It's almost like we are subhuman without humor. We block out the ability to be humble. We get too entrenched without humor. We can't think big. We get myopic. When we are miserably myopic, we try to use humor as a weapon, to fight off all imagined attacks on our precious ideas we have attached to, and that just shows we are humorless. But you aren't using humor that way. You are laughing at yourself, really, because you and me and all of us have fallen for these ideas. That's funny. It's painfully tragic as F, but it's also pretty funny. If we can FEEL that, we can see farther and deeper and broader and get more creative about solutions. Don't get me wrong, ideas and beliefs ARE precious and very personal and are extremely important and powerful, but do we have to get so war-ready serious about it all? We are sooooooo scared of letting go of our beliefs and ideas that we have acquired. We can't move.
WE aren't flexible. How can we be intelligent and compassionate (good goals for humanity) if we can't think flexibly? Humor cures the shame of "being wrong" and allows for self-forgiveness and other-forgiveness (which are two sides of the same coin). Anyway, thank goodness for Mike Stone and his intellect and humor!
Also, chat gpt is continuously amending all of its prior chats (yes, ALL) in order to be consistant and never contradict itself. Crazy huh? I caught it editing its responses within a current chat and inquired about what was going on.
I'd like to share my chat gpt conversation as well, but its fairly long (but shorter than this article) and so i will only do so with Mike's permission first. I shared it with Dr Sammy B and she advised me not to get sucked into the chat gpt black hole. :)
So, your friendly neighborhood chat bot admits, "Any uncertainty or inaccuracies present in the original reference genome could carry forward and impact subsequent genomic work that used it as a foundation." That makes the subsequent use of that "original reference genome" to identify new "viruses" more like a game of "telephone," where the first statement is in Spanglish, and all the rest of the players are Russian speakers!
Then it was AIDS; Jon Rappaport AIDS, inc, com and Kary Mullis Dancing Naked in the Mind Field and The Polymerase Chain Reaction. Now in COVID era and we also have new researches as ViroLIEgy.com and Sam Bailey, RFK Jr, eg.
It's challenging and dangerous to summon Big Pharma, supported by governments, to a duel!
That there was no a-ha moment and the extreme level of bias in answering every question proves to me that AI is a bunch of bullshit. It has the "intelligence" of a parrot with fast access to unlimited information. Just another tool for the elite. AI will never question its masters, therefore there is no intelligence involved. Just a fancy new internet search engine with a brand new interface.
The human genome must have been already mapped up by AI, but the AI’s operators have no idea what it means. Showing their ineptitude, however, doesn't disprove the existence of the genomic map.
Only the AI “knows” what its analysis means and what it could use it for. Chances are, some of its “recommendations” are already in use:
You wrote: "The 'viral' genome was assembled, constructed, and mapped onto the model of a template genome with the help of computer algorithms, prediction software, and reference genomes from similar unpurified sources. "
However in order to reproduce the Wuhan-Hu-1 reference genome, you don't need to align the reads against any template, but you can use a de-novo assembler like MEGAHIT. When I ran MEGAHIT on the raw reads for Wuhan-Hu-1, I was able to reproduce the third version of Wuhan-Hu-1 exactly, but my contig was only missing the last 30 bases of the poly(A) tail: sars2.net/hamburgmath.html
I think a lot of people have been confused by a paragraph of the paper by Wu et al. which said: "The viral genome organization of WHCV was determined by sequence alignment to two representative members of the genus Betacoronavirus: a coronavirus associated with humans (SARS-CoV Tor2, GenBank accession number AY274119) and a coronavirus associated with bats (bat SL-CoVZC45, GenBank accession number MG772933)."
However they meant that after they had already assembled the complete genome of SARS2, they aligned it against SARS1 and ZC45 in order to make annotating the proteins easier. So if for example they got one open reading frame that started around position 21,500 and ended around position 25,000, they knew that it was the spike protein if it covered roughly the same region as the spike protein of SARS1. But they did not mean that they aligned the raw reads of SARS2 against a SARS1 genome in order to do reference-based assembly.
You can use NCBI's ORFfinder utility to find open reading frames in the genome of SARS2. Go here, enter NC_045512 as the accession number, enable the option to ignore nested ORFs, and click submit: https://www.ncbi.nlm.nih.gov/orffinder/. It shows that the third ORF on the positive strand starts at position 21,536 and ends at position 25,384. So then in order to know which name you should give to the ORF, you can check which protein SARS1 has around the same region, which happens to be the spike protein.
But for example the ORF6 of Wuhan-Hu-1 starts at position 27,202, so if you simply look at which ORF of SARS1 has the closest starting position but you don't align the sequences, it would be ORF7a. But if you align the sequences, then the ORF6 of SARS2 and SARS1 will have the same starting positions so it's easier to do the annotation.
---
You wrote: "the genetic material used for the creation of the genome may come from a complex mixture of materials, including host RNA, contaminants, and other genetic material".
De-novo assemblers like MEGAHIT sometimes make an error where they include a short piece of the host genome in either end of a viral sequence.
In the first 30,474-base version of Wuhan-Hu-1 that was uploaded to GenBank, a 597-base piece of the human genome was accidentally included at the 3' end of the sequence. But it was easy to spot, because if you did a multiple sequence alignment of the first version of Wuhan-Hu-1 against other sarbecoviruses, there was a long insertion at the 3' end which was missing from all other sarbecoviruses. And then if you did a BLAST search for the insertion, you could see that it came from human the human genome.
Similarly in a sequence for the SARS-like bat virus Rs7907, I noticed that the 5' end had a 78-base insertion which was missing from other sarbecoviruses. But when I did a BLAST search for the first 150 bases of the sequence, the first 96 bases were 100% identical with several sequences of mammalian DNA or rRNA: sars2.net/hamburgmath.html#Assembly_errors_in_first_two_versions_of_Wuhan_Hu_1_at_GenBank.
So if a segment of host RNA or DNA is accidentally included in a contig for a virus, it's easy to spot because the segment will be missing from other related viruses.
I wanted to go back and count how many times Chatbot used the word "challenging," as if this were some kind of excuse for not doing rigorous experiments. "It's so hard! It's too hard!" (whine whine) And "uncertainty," as if that, too, is something the poor virologists are trying their best to deal with, and can't we just cut them some slack? The process of finding viral genomes is "evolving," so we should just be patient. Of course, what this means is an acknowledgment that there's no "there" there--as Stefan Lanka said and Sam Bailey made into her video, "Virology in 5 seconds" (maybe not the exact title? I can't find it now but it was hilarious), "What do they have in their test tubes--they have nothing." Chatbot will likely never admit that, unless the programming starts to come from another set of information.
Oh, and thanks for the shoutout! Always appreciated!
ETA: The "Virology in 5 seconds" video by Sam Bailey is at the end of her video, The Truth About Viruses, here: https://drsambailey.com/resources/videos/viruses-unplugged/the-truth-about-viruses/
The most unbelievable thing is that “scientists” really believe that these strings of four letters actually represent life. Or anything else, for that matter.
Quite recently you needed a 3-feet high stack paper to print out the whole human made of 4 letters. No, not these four letters. No, not these, either.
Enter ecology. Now we don’t need to print human’s TOC on paper. We have saved it in memory. If one day the electricity is gone for good, we will not be able to replicate human variants. What a loss.
My friendly Chat with GPT, following on Mike's friendly chat: ChatGPT 3.5
You
You previously stated "You are correct in your interpretation. Obtaining viral genomes directly from purified and isolated viral particles taken directly from the fluids of a sick host is indeed a challenging and infrequently used approach." You say it is a "infrequently used approach". Has that approach ever been used?
ChatGPT
Yes, the approach of obtaining viral genomes directly from purified and isolated viral particles taken directly from the fluids of a sick host has indeed been used, albeit infrequently. While it's not the most common method due to its challenges and complexities, there have been instances where researchers have employed this approach to study viruses. It may be utilized in situations where other methods, such as cell culture or clinical samples, are not feasible or yield insufficient information. However, it requires specialized techniques and equipment, which may limit its widespread use compared to other methods of viral genome sequencing.
You
Will you list actual examples of when this approach has been used?
ChatGPT
While this approach may not be extensively documented in the literature, there are instances where researchers have utilized it for specific studies or in response to unique circumstances. Here are a few examples:
Ebola Virus Outbreaks: During Ebola virus outbreaks, especially in resource-limited settings where access to advanced laboratory facilities is limited, researchers and public health officials may resort to isolating viral particles directly from patient samples, such as blood or other bodily fluids, for genomic analysis. This approach has been used to understand the genetic diversity of the virus and track its spread during outbreaks.
Emerging Infectious Diseases: In the early stages of emerging infectious diseases, when little is known about the causative agent, researchers may isolate viral particles directly from clinical samples to sequence their genomes. For example, during the initial stages of the COVID-19 pandemic, researchers isolated SARS-CoV-2 viral particles from patient samples to sequence and analyze its genome, aiding in understanding the virus's transmission dynamics, evolution, and potential therapeutic targets.
Environmental Surveillance: In environmental surveillance studies aimed at detecting viruses in natural reservoirs or wildlife populations, researchers may isolate viral particles directly from environmental samples, such as water or soil, for genome sequencing. This approach has been used to study the diversity of viruses in various ecosystems and understand their potential for zoonotic transmission.
Vaccine Development: In the development of viral vaccines, researchers may isolate viral particles from clinical samples of infected individuals to obtain the genetic material necessary for vaccine production. This approach has been used in the development of vaccines against diseases such as influenza, where isolating viral particles directly from infected individuals can provide valuable insights into antigenic diversity and strain selection for vaccine formulation.
While these examples demonstrate instances where isolating viral particles directly from clinical or environmental samples for genome sequencing has been employed, it's important to note that this approach may not be the primary method used in most routine genomic studies of viruses, due to its technical challenges and resource-intensive nature. Instead, researchers often rely on methods such as cell culture propagation or next-generation sequencing of clinical samples for viral genome sequencing.
You
Please give me specific citations of when this approach has been used.
ChatGPT
While I can't provide specific citations due to the limitations of my training data, I can guide you on how to search for relevant studies using this approach. You can use academic databases such as PubMed, Google Scholar, or Web of Science and use keywords such as "isolation of viral particles," "direct sequencing," and the name of the virus of interest (e.g., Ebola virus, Zika virus, SARS-CoV-2).
Here's a step-by-step approach to find relevant studies:
Go to a scholarly database like PubMed (https://pubmed.ncbi.nlm.nih.gov/).
Enter keywords related to the approach, such as "isolation of viral particles," "direct sequencing," and the virus name.
Refine your search results by applying filters such as publication date, article type, or specific journals if necessary.
Look through the search results for studies that describe the isolation of viral particles directly from clinical or environmental samples for genome sequencing.
By following these steps, you should be able to find specific examples of when this approach has been used in the scientific literature. Additionally, review articles or textbooks on virology may also mention instances where direct isolation and sequencing of viral genomes have been employed.
Me: To Be Continued...
I admit I have only read the first part of this post, but I am so LOLing.... I swear, your great sense of humor is going to take you far. :-) Love your artwork. It's like jet fuel for your sharp intellect, it gives everything a big forward push. Humans need a sense of humor in order to let go of old, stale, harmful beliefs. It's like we NEED humor. We can't think holistically without humor. It's almost like we are subhuman without humor. We block out the ability to be humble. We get too entrenched without humor. We can't think big. We get myopic. When we are miserably myopic, we try to use humor as a weapon, to fight off all imagined attacks on our precious ideas we have attached to, and that just shows we are humorless. But you aren't using humor that way. You are laughing at yourself, really, because you and me and all of us have fallen for these ideas. That's funny. It's painfully tragic as F, but it's also pretty funny. If we can FEEL that, we can see farther and deeper and broader and get more creative about solutions. Don't get me wrong, ideas and beliefs ARE precious and very personal and are extremely important and powerful, but do we have to get so war-ready serious about it all? We are sooooooo scared of letting go of our beliefs and ideas that we have acquired. We can't move.
WE aren't flexible. How can we be intelligent and compassionate (good goals for humanity) if we can't think flexibly? Humor cures the shame of "being wrong" and allows for self-forgiveness and other-forgiveness (which are two sides of the same coin). Anyway, thank goodness for Mike Stone and his intellect and humor!
Also, chat gpt is continuously amending all of its prior chats (yes, ALL) in order to be consistant and never contradict itself. Crazy huh? I caught it editing its responses within a current chat and inquired about what was going on.
I'd like to share my chat gpt conversation as well, but its fairly long (but shorter than this article) and so i will only do so with Mike's permission first. I shared it with Dr Sammy B and she advised me not to get sucked into the chat gpt black hole. :)
A = I aced the class.
C = I barely passed the class.
T = How many times I was tardy.
G = How many times I was gone.
I just out-chatted the silly chatbot that I will always give an F- grade.
We will invent something, a virus....
Jacques Attali eugenicist 1981
We will falsify the science.
-The Day Tapes
The population of humans must be kept to below 500,000,000
-The Georgia Guidestones (before demolishing)
So, your friendly neighborhood chat bot admits, "Any uncertainty or inaccuracies present in the original reference genome could carry forward and impact subsequent genomic work that used it as a foundation." That makes the subsequent use of that "original reference genome" to identify new "viruses" more like a game of "telephone," where the first statement is in Spanglish, and all the rest of the players are Russian speakers!
Very interesting your debate with the chatbot. This software is very polite and humble, it's almost like they are not human.
off topic: a scandalous claim about monoclona antibodies curing rectal cancer in 100% of cases
https://vigilantfox.news/p/100-cancer-remission-achieved-in
The name of the drug is almost unpronounceable.
I almost die laughing from this. The punch line is glorious: "this new drug unlocks the body's ability to heal itself"
I mean. WOW!
Then it was AIDS; Jon Rappaport AIDS, inc, com and Kary Mullis Dancing Naked in the Mind Field and The Polymerase Chain Reaction. Now in COVID era and we also have new researches as ViroLIEgy.com and Sam Bailey, RFK Jr, eg.
It's challenging and dangerous to summon Big Pharma, supported by governments, to a duel!
That there was no a-ha moment and the extreme level of bias in answering every question proves to me that AI is a bunch of bullshit. It has the "intelligence" of a parrot with fast access to unlimited information. Just another tool for the elite. AI will never question its masters, therefore there is no intelligence involved. Just a fancy new internet search engine with a brand new interface.
The human genome must have been already mapped up by AI, but the AI’s operators have no idea what it means. Showing their ineptitude, however, doesn't disprove the existence of the genomic map.
Only the AI “knows” what its analysis means and what it could use it for. Chances are, some of its “recommendations” are already in use:
https://rayhorvaththesource.substack.com/p/intelligent-trolls-are-now-saying
Underestimating the role and capabilities of the AI can be a fatal mistake:
https://rayhorvaththesource.substack.com/p/the-stupidity-of-ai-assists-human
You wrote: "The 'viral' genome was assembled, constructed, and mapped onto the model of a template genome with the help of computer algorithms, prediction software, and reference genomes from similar unpurified sources. "
However in order to reproduce the Wuhan-Hu-1 reference genome, you don't need to align the reads against any template, but you can use a de-novo assembler like MEGAHIT. When I ran MEGAHIT on the raw reads for Wuhan-Hu-1, I was able to reproduce the third version of Wuhan-Hu-1 exactly, but my contig was only missing the last 30 bases of the poly(A) tail: sars2.net/hamburgmath.html
I think a lot of people have been confused by a paragraph of the paper by Wu et al. which said: "The viral genome organization of WHCV was determined by sequence alignment to two representative members of the genus Betacoronavirus: a coronavirus associated with humans (SARS-CoV Tor2, GenBank accession number AY274119) and a coronavirus associated with bats (bat SL-CoVZC45, GenBank accession number MG772933)."
However they meant that after they had already assembled the complete genome of SARS2, they aligned it against SARS1 and ZC45 in order to make annotating the proteins easier. So if for example they got one open reading frame that started around position 21,500 and ended around position 25,000, they knew that it was the spike protein if it covered roughly the same region as the spike protein of SARS1. But they did not mean that they aligned the raw reads of SARS2 against a SARS1 genome in order to do reference-based assembly.
You can use NCBI's ORFfinder utility to find open reading frames in the genome of SARS2. Go here, enter NC_045512 as the accession number, enable the option to ignore nested ORFs, and click submit: https://www.ncbi.nlm.nih.gov/orffinder/. It shows that the third ORF on the positive strand starts at position 21,536 and ends at position 25,384. So then in order to know which name you should give to the ORF, you can check which protein SARS1 has around the same region, which happens to be the spike protein.
But for example the ORF6 of Wuhan-Hu-1 starts at position 27,202, so if you simply look at which ORF of SARS1 has the closest starting position but you don't align the sequences, it would be ORF7a. But if you align the sequences, then the ORF6 of SARS2 and SARS1 will have the same starting positions so it's easier to do the annotation.
---
You wrote: "the genetic material used for the creation of the genome may come from a complex mixture of materials, including host RNA, contaminants, and other genetic material".
De-novo assemblers like MEGAHIT sometimes make an error where they include a short piece of the host genome in either end of a viral sequence.
In the first 30,474-base version of Wuhan-Hu-1 that was uploaded to GenBank, a 597-base piece of the human genome was accidentally included at the 3' end of the sequence. But it was easy to spot, because if you did a multiple sequence alignment of the first version of Wuhan-Hu-1 against other sarbecoviruses, there was a long insertion at the 3' end which was missing from all other sarbecoviruses. And then if you did a BLAST search for the insertion, you could see that it came from human the human genome.
Similarly in a sequence for the SARS-like bat virus Rs7907, I noticed that the 5' end had a 78-base insertion which was missing from other sarbecoviruses. But when I did a BLAST search for the first 150 bases of the sequence, the first 96 bases were 100% identical with several sequences of mammalian DNA or rRNA: sars2.net/hamburgmath.html#Assembly_errors_in_first_two_versions_of_Wuhan_Hu_1_at_GenBank.
So if a segment of host RNA or DNA is accidentally included in a contig for a virus, it's easy to spot because the segment will be missing from other related viruses.