The tip of the ice berg

[Bungle_Bear]

The majority of Germans thought that Hitler was leading them to the promised land. The majority of Russians believe that Putin was justified in invading Ukraine. The majority of North Koreans believe that Kim is the greatest leader ever and some kind of demi-god. The majority is often wrong. And evolution is taught in schools as if it was fact, at least in the education systems that I know of. Teachers in the US have been fired even for pointing out possible objections to evolution. If the theory is so sound, why the fear of examining possible flaws?

The majority view used to be that Christianity was true. Nice to see you accept that it isn't

 

[driewerf]

Home

So, BppLEE preetends that creationists can respect and love science and gives this link as piece of evidence: Home
I went to the website and found creationist and ID related articles, including one about ERV’s. Since I know a tiny little bit about molecular biology, I felt bold enough to open the article and read.
Here is the article in unredacted: Endogenous Retrovirus Expression Evinces Design
Let us see how they fare.

One of my first lab “projects” as a graduate student—assigned to me by my PhD advisor Jack Blazyk—was to clean and organize the lab. This assignment wasn’t out of the ordinary. It is something commonly asked of first-year graduate student plebs. As part of my task, Jack asked me to go through every drawer in the lab, clean them out, and organize the contents.
One of the drawers held equipment for an ultra-microcentrifuge. Among the rotors, microcentrifuge tubes, tools, and other centrifuge parts were several straws that had been cut into pieces. I couldn’t imagine why anyone would put straw pieces in a lab drawer. So, I threw them away. As it turns out, those straw pieces were parts for the pipettes designed to deliver samples to the centrifuge tubes. Oops.
Fortunately, the straw pieces were easily replaced.
Straws aren’t junk. They are designed to make it easier for people to consume beverages. From my perspective, however, the straw pieces in the lab drawer must have been trash, because they were in an unfamiliar and unexpected context. If I saw them in a restaurant I would know of their use immediately. But in a laboratory drawer? Yet when I learned more about how the ultra-microcentrifuge worked, I discovered that the straw pieces weren’t junk at all.

So, a story about how something that seemed junk first turned out be useful. Nice, but not a lot of science involved.

Scientists studying genomes are learning the same lesson I learned all those years ago as a budding graduate student. Sometimes things that appear to be junk are there for a reason. Biologists have long thought that many of the sequence elements in genomes, such as endogenous retroviruses (ERVs), are nothing more than useless junk—the vestiges of an evolutionary history—because they occur in an unfamiliar and unexpected context.
ERVs bear strong sequence similarity to retroviruses, but biologists initially deemed ERVs junk because they are found in genomes, instead of in viral capsids. Yet, life scientists have come to discover that ERVs serve several vital roles, as recent research from Japan attests.1

Fine. A little bit of reference to scientific research. But nothing pointing toward design. Just the fact that scientists thought that ERV’s were useless and some have been found useful.

This insight has important scientific implications because it gives us a deeper understanding about genome biology. It also has important ramifications for those of us who view the human genome (and all genomes) from a design/creation model perspective because it further justifies our position.

How does this confirms the creationist view? The statement that ERV’s are useful is made a few times, but it will never be justified.

But first a quick primer on retroviruses and ERVs for those who need it. If not, feel free to skip ahead to: Can the Occurrence of ERVs Be Explained from a Creation Model Perspective?

That indeed is to be shown. But will never be.
[/quote]Retroviruses
Like all viruses, retroviruses consist of genetic material surrounded by a protein capsid. Retroviruses infect organisms by invading specific cell types of the host organism. After the retroviruses attach to the target cell’s surface, the targeted cell engulfs them. Once engulfed, the viral genetic material exploits the host cell’s machinery to produce copies of the viral genetic material and viral proteins. These biomolecules then assemble into new viral particles. When the newly formed viruses escape from the invaded cell, the infection cycle repeats.
Because the genetic material of retroviruses is RNA, it must be converted into DNA before the infectious cycle can proceed. This conversion is carried out by an enzyme called reverse transcriptase, which is delivered to the target cell along with the retroviral RNA. The enzyme uses the retroviral RNA to make DNA. This newly made DNA can then use the invaded cell’s biosynthetic pathways to direct the production of new retroviral particles. The DNA copy of the retroviral genetic material can also become incorporated into the host cell’s genome. When this insertion takes place, the retroviral DNA becomes part of the host cell’s genome. This process is called endogenization.
Endogenous Retroviruses (ERVs)
Once retroviral DNA becomes incorporated into an organism’s genome it is called an endogenous retrovirus (in contradistinction to exogenous retroviruses, which exist independent of genomes). The endogenous retrovirus can still produce retroviral particles, if its DNA is transcribed by the host cell’s biochemical machinery.
If the ERV infects a germ line cell (a sperm cell or an egg cell), it can be inherited and transmitted from generation to generation as a permanent feature of the genome. If the ERV DNA experiences severe mutations, it becomes disabled and remains in the genome as nonfunctional, junk DNA. [/quote]
A short but fair description of what ERV’s are. I don’t have any ccomment about it.

Endogenous Retroviruses and the Case for Human Evolution
Many human ERVs are also found in the genomes of chimpanzees, bonobos, gorillas, and orangutans. Not only do these ERVs share many of the same sequence patterns, but they also appear in corresponding locations in the genomes. Evolutionary biologists view these patterns as evidence for a shared evolutionary history among humans and the great apes. Accordingly, the shared ancestor (of, say, humans and chimpanzees) became infected by a specific retrovirus that became endogenized. Later, the endogenized retroviruses experienced mutations that disabled them in the ancestor’s genome. The ERV sequences were retained in the genomes of humans and chimpanzees as their separate evolutionary lineages diverged from the common ancestor. According to the model, the endogenous retroviruses shared by humans and chimpanzees represent the molecular artifacts of infections that occurred millions of years ago and left their imprint on contemporary genomes via their shared ancestry.

Again. A short summary but correct. But obviously absent is the reason why that scientists beive that this is an indication of evolution: because all DNA is ingerited from a previous ancestor. Because all DNA you carry is a copy of your dad’d and mo’s DNA, which is a copy of their dad’d and mom’s DNA, which is a copy of their mom’s and dad’s DNA and so on. And if a mutation (or a retrovirus) enters the germ line all descendants will carry that muation.

Can the Occurrence of ERVs Be Explained from a Creation Model Perspective?
For those who advocate for ID or a creation model approach to biology, troubling questions arise: Why would the Creator introduce the same nonfunctional sequence elements in the same locations within the genomes of organisms that naturally group together (based on other biological features)? And why would he create these shared sequence elements to bear such strong similarity to retroviruses?

Wait, the very existence of this creator needs to be proven. Not assumed. Here is the point where BPPLEE fails to prove that creationists rely on science. Here the point to be proven is taken for granted and hence it is cleear again that creationism is a pseudo science.

For many people, the presence and distribution of ERV sequences in genomes provide indisputable evidence for human evolution and our shared ancestry with the great apes.

Indeed, and the ommission of why that is so is a great manco.

Is it possible, however, to account for ERVs from an intelligent design/creation model perspective?
To do so, at minimum those who advocate for a design/creation must:
• demonstrate that ERVs are functional,
• account for the sequence similarity between ERVs and retroviruses, and
• explain their shared distribution in the genomes of organisms that naturally cluster together.

Now, here are thre bulletpoints, and all three of them are suspicious. The first one -useful ERV’s are proof of design, isn’t justified anywhere. I said it already, and I say it again. A beneficiary ERV will provide an evolutionary advantage and will be spread more rapidly through a population. Hence it doesn’t differentiate between the two “models”.
The second and third bullet points will just be dismissed as “the designer did it that way”.

Toward this end, life scientists have recently identified several roles played by ERVs, including providing a defense against retroviral infections. (See Resources for articles detailing some of these functions.)
ERVs Protect Vulnerable Early-Stage Embryos from Viruses
In 2015, researchers from Stanford University showed that a class of ERVs in the human genome (HERV-K) becomes transcriptionally active during the 8-cell stage of human embryos. This activity ceases once the embryo reaches the epiblast stage. During this window of time, the researchers detected gag and rec proteins (encoded by the ERVs) in the blastomeres’ cytoplasm.2 After this stage, the expression of the HERV-K sequences becomes silenced through methylation of their LTR sequences.
The researchers demonstrated that ERV expression affords blastomeres protection against the H1N1 virus by hampering its interaction with the cell membrane and disrupting the early stages of the viral invasion. The production of gag proteins and the ERV RNA also inhibits the retroviral life cycle through competitive inhibition, a process that disrupts the assembly of newly made retroviral virions.
Regulation of ERV Expression Is Fine-Tuned
Work by the Japanese research team builds upon this earlier finding. They discovered that the transcription factor SOX-2 regulates ERV expression by binding to promoter sequences in the LTR sequences of HERV-K sequences. This transcription factor is active during the earliest stages of embryonic development. It maintains the blastomeres in a pluripotent state, in which the cells replicate without differentiating.
By the epiblast stage of embryonic development, SOX-2 expression is shut down. This event allows the embryonic cells to begin the process of differentiation. It also leads to the cessation of ERV transcription. This cessation is important. If ERV expression continues unchecked, then a process called retrotranspositioning occurs, in which the ERV sequences copy themselves continuously and insert randomly throughout the genome. When ERV sequences retrotranspose, they cause damage to the genome that can lead to cancer. Biomedical researchers have discovered that cancer stem cells express SOX-2 at high levels.
As the Japanese team points out, “The strict dependence of HERV-K on SOX-2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos.”3

For those for which the above is TL; DR: scientists have found that a very limited nomber of ERV’s have a useful fuction. This satifies bullet point one. But that point does not differentiate between the Theory of Evolution and the “creation model”.

ERVs in a Creation Model
The results from this study—and others (see the Resources section)—satisfy two of the three criteria required to justifiably interpret the presence of ERVs in genomes from a creation model perspective by (1) demonstrating the functional role of these sequences, and (2) accounting for their close similarity to retroviral genetic material.

No, it doesn’t satisfy point two. Reread what is written. It describes the usefulness of ERV’s, but doesn’t account for the similarity of it with viral DNA, and doesn’t hint at any moment to any design, creation or creator. The authors have been pulling wool over the reader’s eyes by justifying point one (which is not determinant for any of the two models) and hoping that the unattentive reader doesn’t notice the total silence about point two.
Again, BPPLEE proposing that site as proof that creationists use science fails. They’re only good at fooling their audience.

But what about the distribution of ERVs in the genomes of organisms that naturally cluster together into nested hierarchies?
It is true that most life scientists regard shared biological features—including DNA sequences—as evidence for their shared evolutionary ancestry. Yet an alternative explanation for biological similarities can be advanced. Following after the ideas of biologist Sir Richard Owen, shared biological features can be interpreted as manifestations of a common blueprint—an archetype that arises out of the Creator’s mind.

Again, the point to be proven is assumed. Again a big fail for the creationists.

In other words, from a creation model perspective, the Creator intentionally introduced the genetic similarities in the genomes of humans and the great apes. This includes junk DNA sequences, such as ERVs. Accordingly, the corresponding sequence similarities and locations for junk DNA sequences among organisms that naturally group reflect functional considerations.
Even though many biologists can’t imagine why a Creator would add ERV sequences into genomes, deeper insight into ERV biology offers an unexpected explanation.

And this needed to be upto exactly the same base pair for all species? And mimicking an exact nested hierarchy, just like the ToE would demand? And like it mimicks just an inherited pattern, upto the non functional one? Really.
Big Fail.

 

[46AND2]

So, BppLEE preetends that creationists can respect and love science and gives this link as piece of evidence: Home
I went to the website and found creationist and ID related articles, including one about ERV’s. Since I know a tiny little bit about molecular biology, I felt bold enough to open the article and read.
Here is the article in unredacted: Endogenous Retrovirus Expression Evinces Design
Let us see how they fare.

So, a story about how something that seemed junk first turned out be useful. Nice, but not a lot of science involved.

Fine. A little bit of reference to scientific research. But nothing pointing toward design. Just the fact that scientists thought that ERV’s were useless and some have been found useful.

How does this confirms the creationist view? The statement that ERV’s are useful is made a few times, but it will never be justified.

That indeed is to be shown. But will never be.
Retroviruses
Like all viruses, retroviruses consist of genetic material surrounded by a protein capsid. Retroviruses infect organisms by invading specific cell types of the host organism. After the retroviruses attach to the target cell’s surface, the targeted cell engulfs them. Once engulfed, the viral genetic material exploits the host cell’s machinery to produce copies of the viral genetic material and viral proteins. These biomolecules then assemble into new viral particles. When the newly formed viruses escape from the invaded cell, the infection cycle repeats.
Because the genetic material of retroviruses is RNA, it must be converted into DNA before the infectious cycle can proceed. This conversion is carried out by an enzyme called reverse transcriptase, which is delivered to the target cell along with the retroviral RNA. The enzyme uses the retroviral RNA to make DNA. This newly made DNA can then use the invaded cell’s biosynthetic pathways to direct the production of new retroviral particles. The DNA copy of the retroviral genetic material can also become incorporated into the host cell’s genome. When this insertion takes place, the retroviral DNA becomes part of the host cell’s genome. This process is called endogenization.
Endogenous Retroviruses (ERVs)
Once retroviral DNA becomes incorporated into an organism’s genome it is called an endogenous retrovirus (in contradistinction to exogenous retroviruses, which exist independent of genomes). The endogenous retrovirus can still produce retroviral particles, if its DNA is transcribed by the host cell’s biochemical machinery.
If the ERV infects a germ line cell (a sperm cell or an egg cell), it can be inherited and transmitted from generation to generation as a permanent feature of the genome. If the ERV DNA experiences severe mutations, it becomes disabled and remains in the genome as nonfunctional, junk DNA.
A short but fair description of what ERV’s are. I don’t have any ccomment about it.

Again. A short summary but correct. But obviously absent is the reason why that scientists beive that this is an indication of evolution: because all DNA is ingerited from a previous ancestor. Because all DNA you carry is a copy of your dad’d and mo’s DNA, which is a copy of their dad’d and mom’s DNA, which is a copy of their mom’s and dad’s DNA and so on. And if a mutation (or a retrovirus) enters the germ line all descendants will carry that muation.

Wait, the very existence of this creator needs to be proven. Not assumed. Here is the point where BPPLEE fails to prove that creationists rely on science. Here the point to be proven is taken for granted and hence it is cleear again that creationism is a pseudo science.

Indeed, and the ommission of why that is so is a great manco.

Now, here are thre bulletpoints, and all three of them are suspicious. The first one -useful ERV’s are proof of design, isn’t justified anywhere. I said it already, and I say it again. A beneficiary ERV will provide an evolutionary advantage and will be spread more rapidly through a population. Hence it doesn’t differentiate between the two “models”.
The second and third bullet points will just be dismissed as “the designer did it that way”.

For those for which the above is TL; DR: scientists have found that a very limited nomber of ERV’s have a useful fuction. This satifies bullet point one. But that point does not differentiate between the Theory of Evolution and the “creation model”.

No, it doesn’t satisfy point two. Reread what is written. It describes the usefulness of ERV’s, but doesn’t account for the similarity of it with viral DNA, and doesn’t hint at any moment to any design, creation or creator. The authors have been pulling wool over the reader’s eyes by justifying point one (which is not determinant for any of the two models) and hoping that the unattentive reader doesn’t notice the total silence about point two.
Again, BPPLEE proposing that site as proof that creationists use science fails. They’re only good at fooling their audience.

Again, the point to be proven is assumed. Again a big fail for the creationists.

And this needed to be upto exactly the same base pair for all species? And mimicking an exact nested hierarchy, just like the ToE would demand? And like it mimicks just an inherited pattern, upto the non functional one? Really.
Big Fail.

I first found this site many years ago while looking for discussions about ERVs. I think those threads have been deleted now, or at least changed location; my bookmark no longer works. Which is unfortunate because they were very good threads. ERVs and pseudogenes, imo, are the strongest arguments for accepting evolution over special creation, not only because of how beautifully it demonstrates nested hierarchies, because it detracts from the common designer argument. Really? He designed viruses and broken genes into genomes?

 

[AV1611VET]

I first found this site many years ago while looking for discussions about ERVs. I think those threads have been deleted now, or at least changed location; my bookmark no longer works. Which is unfortunate because they were very good threads. ERVs and pseudogenes, imo, are the strongest arguments for accepting evolution over special creation, not only because of how beautifully it demonstrates nested hierarchies, because it detracts from the common designer argument. Really? He designed viruses and broken genes into genomes?

QV please:

This thread is actually how I found the site. I was doing some research on ERVs and this popped up in the Google search.

 

[46AND2]

QV please:

Thanks AV. I hadn't done a search yet. link address must have changed or something since I created that bookmark a decade ago. lol

 

[AV1611VET]

Thanks AV.

My pleasure, sir.

Welcome back!

 

[Frank Robert]

So, BppLEE preetends that creationists can respect and love science and gives this link as piece of evidence: Home
I went to the website and found creationist and ID related articles, including one about ERV’s. Since I know a tiny little bit about molecular biology, I felt bold enough to open the article and read.
Here is the article in unredacted: Endogenous Retrovirus Expression Evinces Design
Let us see how they fare.

So, a story about how something that seemed junk first turned out be useful. Nice, but not a lot of science involved.

Fine. A little bit of reference to scientific research. But nothing pointing toward design. Just the fact that scientists thought that ERV’s were useless and some have been found useful.

How does this confirms the creationist view? The statement that ERV’s are useful is made a few times, but it will never be justified.

That indeed is to be shown. But will never be.

Retroviruses
Like all viruses, retroviruses consist of genetic material surrounded by a protein capsid. Retroviruses infect organisms by invading specific cell types of the host organism. After the retroviruses attach to the target cell’s surface, the targeted cell engulfs them. Once engulfed, the viral genetic material exploits the host cell’s machinery to produce copies of the viral genetic material and viral proteins. These biomolecules then assemble into new viral particles. When the newly formed viruses escape from the invaded cell, the infection cycle repeats.
Because the genetic material of retroviruses is RNA, it must be converted into DNA before the infectious cycle can proceed. This conversion is carried out by an enzyme called reverse transcriptase, which is delivered to the target cell along with the retroviral RNA. The enzyme uses the retroviral RNA to make DNA. This newly made DNA can then use the invaded cell’s biosynthetic pathways to direct the production of new retroviral particles. The DNA copy of the retroviral genetic material can also become incorporated into the host cell’s genome. When this insertion takes place, the retroviral DNA becomes part of the host cell’s genome. This process is called endogenization.
Endogenous Retroviruses (ERVs)
Once retroviral DNA becomes incorporated into an organism’s genome it is called an endogenous retrovirus (in contradistinction to exogenous retroviruses, which exist independent of genomes). The endogenous retrovirus can still produce retroviral particles, if its DNA is transcribed by the host cell’s biochemical machinery.
If the ERV infects a germ line cell (a sperm cell or an egg cell), it can be inherited and transmitted from generation to generation as a permanent feature of the genome. If the ERV DNA experiences severe mutations, it becomes disabled and remains in the genome as nonfunctional, junk DNA. [/quote]
A short but fair description of what ERV’s are. I don’t have any ccomment about it.

Again. A short summary but correct. But obviously absent is the reason why that scientists beive that this is an indication of evolution: because all DNA is ingerited from a previous ancestor. Because all DNA you carry is a copy of your dad’d and mo’s DNA, which is a copy of their dad’d and mom’s DNA, which is a copy of their mom’s and dad’s DNA and so on. And if a mutation (or a retrovirus) enters the germ line all descendants will carry that muation.

Wait, the very existence of this creator needs to be proven. Not assumed. Here is the point where BPPLEE fails to prove that creationists rely on science. Here the point to be proven is taken for granted and hence it is cleear again that creationism is a pseudo science.

Indeed, and the ommission of why that is so is a great manco.

Now, here are thre bulletpoints, and all three of them are suspicious. The first one -useful ERV’s are proof of design, isn’t justified anywhere. I said it already, and I say it again. A beneficiary ERV will provide an evolutionary advantage and will be spread more rapidly through a population. Hence it doesn’t differentiate between the two “models”.
The second and third bullet points will just be dismissed as “the designer did it that way”.

For those for which the above is TL; DR: scientists have found that a very limited nomber of ERV’s have a useful fuction. This satifies bullet point one. But that point does not differentiate between the Theory of Evolution and the “creation model”.

No, it doesn’t satisfy point two. Reread what is written. It describes the usefulness of ERV’s, but doesn’t account for the similarity of it with viral DNA, and doesn’t hint at any moment to any design, creation or creator. The authors have been pulling wool over the reader’s eyes by justifying point one (which is not determinant for any of the two models) and hoping that the unattentive reader doesn’t notice the total silence about point two.
Again, BPPLEE proposing that site as proof that creationists use science fails. They’re only good at fooling their audience.

Again, the point to be proven is assumed. Again a big fail for the creationists.

And this needed to be upto exactly the same base pair for all species? And mimicking an exact nested hierarchy, just like the ToE would demand? And like it mimicks just an inherited pattern, upto the non functional one? Really.
Big Fail.[/QUOTE]
You deserve a lot of credit for trying to explain science to the uninitiated but their focus is not on science but apologetics, motivated by religious belief, to provide their followers a reason to deny the evolution. As long as the donations keep roiling in and the creationist books keep selling they will continue traffic in pseudo science.