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Friday, 12 June 2026

Junk DNA even more fully salvaged?

 More Functions Reported for Repeat “Junk” DNA


Casey Luskin June 11, 2026

A new paper in PNAS, “CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression,” elaborates more functions for supposed “junk DNA” as helping to create functionally relevant structures in DNA. Last year I wrote about non-B DNA (see here and here). It doesn’t necessarily exhibit the typical double-helical DNA structure, but it can form unique shapes that contribute to a variety of important genomic functions. This new paper explores a structure called the G-quadruplex (G4s), a loop shape that often arises in DNA segments rich in guanine. The paper reports that G4s can perform a variety of functions: 

"G4 binding activities in genomic regulators of nucleosome remodeling, paraspeckle assembly, RNA splicing, and three-dimensional genome organization. Among the prominent hits, we identify the genomic architectural protein, CCCTC-binding factor (CTCF), as one of the strongest G4 binders."

The latter function is crucial, as it reflects the ability of G4 structures to regulate large-scale chromosomal structures:

"G-quadruplexes interact with several nuclear protein complexes involved in crucial genomic processes. We found that the genomic architectural protein, CCCTC-binding factor (CTCF), directly binds to G4s and this interaction is important for regulation of genome topology and gene expression. Our work uncovers the architectural roles of G4 structures in the genome and contributes important insights into G4 biology and 3D genome organization."

A Variety of Genomic Functions

Thus, these G4 structures contribute to a variety of genomic functions, and importantly they help form topologically associating domains (TADs) that control the 3D structure of the genome:

"At the scale of tens to hundreds of kilobases, the genome is further assembled into self-interacting regions known as topologically associating domains (TADs), with higher propensity of genomic interactions observed within, rather than between TADs. TADs mediate enhancer–promoter interactions and are important for cell-type specific gene expression programs. Interestingly, G4s are shown to be enriched at TAD boundaries and implicated in regulating insulation strength of TADs"

The paper proposes a model that involves “CTCF–G4 interaction in mediating long-range chromatin looping to define stable chromatin loops or boundaries of topologically associating domains (TADs).”

So Why Does This Matter?

A variety of papers note that repetitive DNA — the precise type of DNA that our junk-DNA-defending friends assure us must be functionless — is vital for forming these G4 structures:

Ambrus et al. (2006): Discusses how telomeric repeats in humans form G-quadruplexes.

Bryan (2020): Reviews how telomeric repeat DNA forms G-quadruplexes

 Waisertreiger et al. (2025):: Discusses how pericentromeric tandem repeat DNA forms G4s.

:Nakagama et al. (2006) Discusses how guanine-rich short tandem repeat DNA forms G4s.

:Piazza et al. (2017):  Zhou et al. (2014): Discusses how the repetitive DNA sequence “GGGGCC” forms G4s.

:Adrian et al. (2014):  Explains how minisatellite tandem repeat sequences contribute to G-quadruplex formation.

: Shows how a minisatellite repeat sequence forms G4s.

:  Raguseo et al. (2023): Explains how the repeat DNA sequence “GGGGCC” forms G4s.

:Bauer et al. (2011): (2011): Shows that repetitive telomeric sequences form G4s.

:Geng et al. (2024): Shows G4s are formed by repeat DNA.

These papers demonstrate that various types of repetitive DNA, including in telomeres, minisatellites, pericentromeric repeats, and other tandem repeat DNA sequences, help form G4 structures. The point being: repetitive DNA helps form non-B DNA shapes like G4s, and these G4s are crucial for defining TADs which help define the 3D structure of the genome, regulating gene expression and even defining cell types. Far from being junk, this repetitive DNA is crucial for formatting the genome.

The genome is rich in function, and we dare not simply dismiss any of it.

Jesus is good and therefore God?

 

Made new by JEHOVAH.

 

Sunday, 3 August 2025

On Isaac Newton's Arianism

 Yes, Sir Isaac Newton held beliefs aligned with Arian theology, though he kept these views private due to their controversial nature. Arianism, based on the teachings of Arius, denies the full divinity of Jesus Christ, asserting that the Son is a created being, subordinate to God the Father. Newton’s extensive theological writings, including manuscripts like A Historical Account of Two Notable Corruptions of Scripture, reveal his rejection of the traditional doctrine of the Trinity. He argued that the concept of the Trinity was not supported by early Christian texts and was a later corruption of scripture, a position central to Arian thought.

Newton’s studies of early Church history and biblical texts led him to conclude that passages like 1 John 5:7, which supports the Trinity, were later interpolations. He believed the original Christian doctrine was closer to Arianism, emphasizing the unity and supremacy of God the Father. However, as a fellow at Trinity College, Cambridge, and a public figure, Newton was cautious, sharing his views only with close associates to avoid persecution, as Arianism was considered heretical in 17th-century England.

His theological notes, many of which were unpublished during his lifetime, confirm his sympathy for Arian ideas, though he never formally declared himself an Arian. Instead, he framed his beliefs as a return to a purer, original Christianity. For further details, Newton’s manuscripts at the National Library of Israel or the Keynes Collection at Cambridge provide primary source material.


The origin of life vs. Darwin

 

Saturday, 19 July 2025

Grok on open theism.

 Open theism, also known as open theology or free will theism, is a theological framework that emphasizes God’s relational nature and the openness of the future. It holds that God is omniscient, omnipotent, and omnibenevolent but chooses to limit His foreknowledge or control over human decisions to allow for genuine free will. Key points:

Open theism, also known as open theology or free will theism, is a theological framework that emphasizes God’s relational nature and the openness of the future. It holds that God is omniscient, omnipotent, and omnibenevolent but chooses to limit His foreknowledge or control over human decisions to allow for genuine free will. Key points:

God’s Knowledge and the Future: Open theism posits that the future is not entirely fixed or exhaustively known by God. Instead, God knows all possibilities and probabilities but leaves room for human free choices, making the future partly "open" or undetermined.

Divine-Human Relationship: God interacts dynamically with creation, responding to human actions in real-time rather than following a predetermined script. This makes prayer, decisions, and actions meaningful, as they can influence outcomes.

Biblical Basis: Proponents cite scriptures where God appears to change His mind (e.g., Exodus 32:14), expresses surprise (e.g., Jeremiah 3:7), or tests people to discover their choices (e.g., Genesis 22:12), suggesting a relational rather than deterministic view.Critiques: Critics, often from classical theism (e.g., Calvinism), argue it undermines God’s sovereignty or omniscience, claiming an all-knowing God must know the future exhaustively. Open theists counter that God’s omniscience includes all that is knowable, but an open future is inherently unknowable in detail.

Key Figures: Theologians like Clark Pinnock, John Sanders, and Gregory Boyd have been influential in developing and defending open theism.It’s a minority view within Christianity, often debated for its implications on divine providence, prophecy, and human responsibility. If you want a deeper dive into specific arguments, biblical texts, or criticisms, let me know!


On evolution and the design debate.


Saturday, 12 July 2025

File under "well said" CXIX

"The end of Life is to become like God,and the Soul following God will become like him."

Socrates.

Tuesday, 8 July 2025

Grok on the history of EVs

 The earliest electric vehicles (EVs) date back to the 19th century, predating modern gasoline cars. Here’s a concise overview:1830s: Robert Anderson, a Scottish inventor, is credited with creating one of the first crude electric carriages around 1832–1839, powered by non-rechargeable primary cells.

1840s–1880s: Inventors like Thomas Davenport and Gustave Trouvé developed early electric motors and vehicles. In 1881, Trouvé showcased an electric tricycle in Paris.

1880s–1890s: Rechargeable lead-acid batteries spurred EV development. In 1884, Thomas Parker built an electric car in England. By the late 1880s, companies like the Electric Carriage and Wagon Company in the U.S. produced electric taxis.

1890s–1900s: EVs peaked in popularity, especially in urban areas, due to their quiet operation and ease of use compared to steam or gasoline vehicles. In 1900, about 28% of U.S. cars were electric, with manufacturers like Studebaker and Columbia producing models.

Decline: By the 1910s, EVs waned due to limited battery range (20–40 miles), high costs, and the rise of affordable gasoline cars like the Ford Model T, coupled with improved road infrastructure favoring longer-range vehicles.

EVs saw a revival in the late 20th century with models like GM’s EV1 (1996), but the modern era began with the Tesla Roadster (2008) and Nissan Leaf (2010), driven by advancements in lithium-ion batteries.


Saturday, 5 July 2025

ID triumps despite the scopes trial

 Despite Scopes Effect, Intelligent Design Flourishes


The Scopes “Monkey” trial of 1925 has cast a long shadow over the evolution debate in the last century, thanks in large part to the Hollywood film Inherit the Wind, which caricatured the trial and promoted stereotypes that still persist today. On a new episode of ID the Future, I continue a conversation with Dr. Casey Luskin about the long history of the Scopes effect in science and how intelligent design has managed to flourish in spite of it.

In Part 2, Dr. Luskin explains that even as Scopes stereotypes were crystallizing in the public consciousness, skepticism about the power of Darwin’s selection/mutation mechanism continued to mount, and not just in intelligent design circles. Prominent evolutionary biologists were also voicing concern about the adequacy of the modern synthesis of Darwin’s theory. And as those concerns grew louder, so did the desperate response from committed Darwinists. Luskin talks about a surge of persecutions that have been leveled against any scientist who dares to question neo-Darwinism. 

But, as Luskin notes, the intelligent design research project has gone from strength to strength in the last three decades. Much progress has been made in building a strong, cumulative case for intelligent design as the best explanation for the origin and development of life on Earth. So as the Scopes centennial gets marked with fanfare in 2025, do ID scientists get a seat at the table? Or is the spirit of Scopes still hampering scientific progress and academic freedom today? Luskin has answers. Download the podcast or listen to it here.

Thursday, 3 July 2025

The state religion?

 More on Disguised Religion


Not in science or in any other context does one faith get to impose its terms on others. That sounds like common sense. But a concern about being scientifically or politically acceptable often causes us to feel intimidated into accepting disguised religious terms that are not our own, when we’re really under no obligation to do so. With that in mind, I want to highlight a post here from earlier today, “Methodological Naturalism as religion in Disguise.” 

The key point: “If the observable data points to outcomes that natural causes cannot adequately explain, then ruling out supernatural causes from the outset is not scientific humility — it’s dogma.”

A Random Example

Religion in disguise is more common than you might think. As a random example, the other day on our Seattle NPR station I was listening to an interview with a local trans activist. The activist, Danni Askini, was saying that trans identity is not a medical practice but a spiritual one. As the activist candidly said, it is a religion where the essential activity is not going to church but going to the doctor (whether for surgery or medication). I don’t think that Askini, who goes by “they/she,” had fully thought through the implications. If trans is a religion, then you don’t have the right to tell others to accept your preferred religious language, and call you “she” rather than the more biologically accurate “he,” or to adhere to your preferred framing of reality at all.

That is a scientific context, since biology is a science, but in the philosophical scientific context of methodological naturalism (MN), adherents of the dogma, whether atheists or theistic evolutionists, don’t get to dictate to others that they must accept the framing where only natural, never supernatural, causation is scientifically acceptable. We outside the walls of MN always have to bear that in mind. Mutual respect is one thing. Dictating terms is another.