So here we go again. Yet another blog page containing the same old lie as usual from the creationist/ID mob. My comments in red. Their text in black.
The lie? That 'evolutionsts' claim that endogenous retroviruses are 'junk', and to find any function in them puts doubt on the conclusion that they are inherited remnants of retroviral integrations with our DNA.
BTW, "Evolution News" is a deceptively misleading title. It does not report on evolutionary science, but pumps out valueless propaganda against evolutionary science.
EVOLUTION
INTELLIGENT DESIGN
Waste Not: Research Finds that “Far from Junk DNA,” ERVs Perform “Critical Cellular Functions”
In the past, reporting by Evolution News has documented a variety of important functions for endogenous retroviruses (ERVs) and other transposable elements and retrotransposons.
The writer cannot claim that Evolution News has done anything more than point to mainstream research on this, and then apply its spin. 'Intelligent Design' produces no research and publishes no original findings whatsoever. It is entirely parasitic on the science it tries to discredit. The findings of function in these elements were discovered by mainstream (real) scientists who published them. So much for the global, multi-generational conspiracy to pull the wool over our eyes concerning evolution.
These, of course, have frequently been called “junk DNA,” mere evolutionary waste or flotsam, by critics of intelligent design.
No, they have not. They have been identified as inherited remnants of retroviral integrations by researchers, and not because they aim to criticise 'Intelligent Design' (ID). ID is totally irrelevant to their work.
Evidence of this widespread function is nothing new. As a 2017 paper in Nature Reviews Genetics noted, “Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs.”
The writer cannot claim that Evolution News has done anything more than point to mainstream research on this, and then apply its spin. 'Intelligent Design' produces no research and publishes no original findings whatsoever. It is entirely parasitic on the science it tries to discredit. The findings of function in these elements were discovered by mainstream (real) scientists who published them. So much for the global, multi-generational conspiracy to pull the wool over our eyes concerning evolution.
These, of course, have frequently been called “junk DNA,” mere evolutionary waste or flotsam, by critics of intelligent design.
No, they have not. They have been identified as inherited remnants of retroviral integrations by researchers, and not because they aim to criticise 'Intelligent Design' (ID). ID is totally irrelevant to their work.
Evidence of this widespread function is nothing new. As a 2017 paper in Nature Reviews Genetics noted, “Transposable elements (TEs) are a prolific source of tightly regulated, biochemically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs.”
Now a pair of new articles in Nature Genetics acknowledge just how widespread ERV and retrotransposon functionality is. One is a research paper and the other is a summary article. The summary article opens by explicitly denying that retrotransposons are junk DNA:
Far from being junk DNA, the pervasive retrotransposons that populate the genome have a powerful capacity to influence genes and chromatin. A new study demonstrates how the transcription of one such element, HERV-H, can modify the higher-order 3D structure of chromatin during early primate development.
So make up your mind. Is science claiming that these elements are junk, or not?
The summary further notes that “many ERVs have been co-opted for critical cellular functions.” It reviews some of these functions:
For example, ERVs frequently act to distribute regulatory information and thus confer genes with new patterns of expression and function. Similarly, multiple ERVs have been re-purposed as novel genes themselves, including the ERV envelope-derived syntactins that drive trophoblast fusion and establish the placental fetal–maternal interface. Now, Zhang et al. have identified an additional activity of co-opted ERVs — the alteration of the genome’s 3D structure itself — that may have the capacity to substantially affect gene regulation.
Research and Rhetoric
Looked at from a rhetorical perspective, Nature Genetics is clearly very sensitive about the implications of the study. After all, it shows that ERVs have extremely important functions, which is a bitter pill for many ID opponents. Nearly every time the summary describes an ERV as “functional” the word “co-opted” exapted is the word is placed nearby just to remind you that the ERVs really started off as something like junk
There's that lie again. ERVs start off as retroviral proviruses.
and were “co-opted” exapted by evolution to have a function. Words like “co-opted” are what the late National Academy of Sciences member Philip Skell called called in The Scientist “narrative gloss” — words that have no explanatory value but are brought in after the fact to make a connection to evolution. As Skell wrote:
I found that Darwin’s theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.
Yet another lie. Go to the link to "The Scientist" that they provide. Skell makes no mention of "co-option" or exaptation. The sole purpose of the above passage is to cast spurious, irrelevant assertions .
Far from being uninformative, it provides the only viable explanation of why we find functionality for host organisms in ERVs. The alternative is that some designer - (let's not fool ourselves, the designer is a god - specifically the creationist version of "God") - some designer designed these elements. If anyone wishes to make an actual case for the latter, there is a list of questions at the foot of this page that must be answered satisfactorily if the "design" hypothesis is to be taken seriously. This is a challenge to the ID "scientists". Show us how well your paradigm explains the phenomena we observe. Unlike your blog, this one is open to comments. You can provide your answers here.
To understand the nature of their function, one must turn to the research itself.
The research paper here, “Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells,” starts by noting that the three-dimensional structure of chromosomes is crucial for building gene regulatory networks in animals:
The three-dimensional organization of chromosomes enables long-range interactions between enhancers and promoters that are critical for building complex gene regulatory networks in multicellular species.
That opening comment by itself refutes claims from some evolutionists that the shared three-dimensional structure of chromosomes across different species — often called synteny — is meaningless and reflects only their common ancestry, rather than important functional requirements. But as the paper explains, the three-dimensional organization of chromosome is “critical” for building gene regulatory networks (GRNs) that govern the development and growth of an organism.
More irrelevancies.
More irrelevancies.
Moving Right Along
Good idea.
The paper explains that chromosomes have “a dynamic but non-random hierarchical structure” where they are organized into transcriptionally active, and transcriptionally silent regions. These regions are further broken down into “topologically associating domains (TADs),” which are basically chromosome regions that have important “intradomain interactions.” TAD domains are cell-type specific and species specific — in other words specifying domains of chromosome activity helps determine what kind of proteins will be produced, which helps determine what kind of cell a cell will become. Specified cell types ultimately produce tissues, which produce organs, which produce physiological systems, which produce an organism, which define a species. It’s all hierarchically regulated and it starts at the level of chromosomes with TAD domains.
The paper explains that chromosomes have “a dynamic but non-random hierarchical structure” where they are organized into transcriptionally active, and transcriptionally silent regions. These regions are further broken down into “topologically associating domains (TADs),” which are basically chromosome regions that have important “intradomain interactions.” TAD domains are cell-type specific and species specific — in other words specifying domains of chromosome activity helps determine what kind of proteins will be produced, which helps determine what kind of cell a cell will become. Specified cell types ultimately produce tissues, which produce organs, which produce physiological systems, which produce an organism, which define a species. It’s all hierarchically regulated and it starts at the level of chromosomes with TAD domains.
Sound Designed to You?
TAD boundaries on chromosomes are marked by bundles of proteins, some of which are called CCCTC-binding factors (CTCFs). And it turns out that CTCF binding locations on chromosomes are often controlled by so-called “transposable elements” — those supposed junk (there's that lie yet again) DNA elements that make up some 50 percent of the genome. But how important are transposable elements for this role? The paper notes that “how much transposable elements play a role in shaping the genome architecture during evolution has yet to be directly tested, particularly in primates.” Again, the words “during evolution” are more gloss that really just means “important for function.”
ERVs have the same detailed structure as proviruses. This fact does not require us to assume evolution.
Retroviral integration does not target specific loci in DNA. This fact does not require us to assume evolution.
Inheritance places the same genetic material in the same locations in DNA. This fact does not require us to assume evolution.
Evolution is a conclusion from the above facts.The Paper’s Central Finding
Retroviral integration does not target specific loci in DNA. This fact does not require us to assume evolution.
Inheritance places the same genetic material in the same locations in DNA. This fact does not require us to assume evolution.
Evolution is a conclusion from the above facts.The Paper’s Central Finding
And now we come to the central finding of the paper — that a type of endogenous retrovirus (ERV) is critical for defining TAD boundaries:
By interrogating the dynamic remodeling of chromatin architecture during human cardiomyocyte differentiation, we discovered a class of primate-specific endogenous retrotransposons — human endogenous retrovirus subfamily H (HERV-H) — that is involved in establishing TAD boundaries in human pluripotent stem cells (hPSCs). … [C]omparative analysis of the chromatin architecture in primate and non-primate species supports a role for actively transcribed HERV-H elements in demarcating primarily hominid pluripotent stem cell (PSC)-specific TADs. Overall, our results provide direct evidence for retrotransposon elements in actively shaping the chromatin architecture in specific cell types during evolution.
“During evolution”? Right, that’s more gloss, adding nothing to the empirical findings of this study. Again, these ERVs are crucial for defining TAD domain boundaries, which helps shape chromosome architecture, which helps determine cell types, which, as we saw, form the crucial foundation for a hierarchically controlled network that ultimately builds an organism. Here’s the research paper’s conclusion:
Here, we provide multiple lines of evidence showing that the primate-specific HERV-H retroviral elements can delineate TAD boundaries in hPSCs. Previous studies suggested that HERV-H elements integrated into the human genome during primate evolution to regulate human-specific pluripotency by creating novel chimeric transcripts (ESRG, linc-ROR and LINC00458) and providing potential binding sites to recruit pluripotency factors (NANOG, SOX2 and POU5F1). However, our findings indicate that HERV-H sequences may affect gene regulatory programs by also creating new hPSC-specific TAD boundaries that shape the chromatin architecture…. [O]ur findings suggest the intriguing possibility that other endogenous retrovirus families of repeats and/or other families of repetitive elements may have similar abilities to create TADs and insulation.
Evolutionary detritus is what neo-Darwinian theory would expect, but it’s not what we find. ERVs play extremely important functional roles in humans and many other animals. That’s not bad for something that great numbers of evolutionists have told us for decades is nothing more than junk (liar) DNA.
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