Friday, 28 March 2025
Junk DNA =Junk science?
Nobelist Thomas Cech on “Junk RNA”
We can add Nobel Prize-winning biochemist Thomas Cech to the ever-growing list of scientists who reject the “junk DNA” paradigm. Or, more pertinently, the junk RNA paradigm. RNA tends to get left as sidenote in most discussions of genetics, much to Cech’s annoyance — Dr. Cech has always been more in interested in RNA than most of his colleagues, which led him to co-win the Nobel Prize in 1989 for discovering RNA’s catalytic powers.
Adventures with RNA
Now Cech as written a book, The Catalyst: RNA and the Quest to Unlock Life’s Deepest Secrets (W. W. Norton), on his adventures in RNA research. Towards the end he discusses his perspective on the idea of genetic junk. Cech writes
The coding regions of all the human genes that specify proteins make up only about 2 percent of our genome. When we add the introns that interrupt those coding regions — the sequences that are spliced out after the DNA is transcribed into the precursors to mRNA — we account for another 24 percent. That leaves about three-quarters of the genome that is “dark matter.” For decades this 75 percent was dismissed as “junk DNA” because whatever function it had, if any, was invisible to us.
But as technologies for sequencing RNA have improved, scientists have discovered that most of this dark-matter DNA is in fact transcribed into RNA. Some portion of this DNA is copied into RNA in the brain, other portions in muscle, or in the heart, or in the sex organs. It’s only when we add up the RNAs made in all the tissues of the body that we see the true diversity of human RNAs. The total number of RNAs made from DNA’s “dark matter” has been estimated to be several hundred thousand. These are not messenger RNAs, but rather noncoding RNAs — the same general category as ribosomal RNA, transfer RNA, telomerase RNA, and microRNAs. But what they’re doing is still, for the most part, a mystery.
The RNAs that emerge from this dark matter are called long noncoding RNAs (lncRNAs). While they are particularly numerous in humans, they are also abundant in other mammals, including the laboratory mouse. In a few cases, they clearly have a biological function. For example, a lncRNA called Firre contributes to the normal development of blood cells in mice; an overabundance of Firre prevents mice from fending off bacterial infections, as their innate immune response fails. Another lncRNA, called Tug1, is essential for male mice to be fertile. But such verified functions are few and far between. The function of most lncRNAs remains unknown.
As a result, many scientists do not share my enthusiasm for these RNAs. They think that RNA polymerase, the enzyme that synthesizes RNA from DNA, makes mistakes and sometimes copies junk DNA into junk RNA. A more scholarly description of such RNAs might explain them away as “transcriptional noise” — the idea being, again, that RNA polymerase isn’t perfect. It sometimes sits down on the wrong piece of DNA and copies it into RNA, and that RNA may have no function. I readily admit that some of the lncRNAs may in fact be noise, bereft of function, signifying nothing.
However, I’ll point out that there was a time in the not-too-distant past when telomerase RNA and microRNAs and catalytic RNAs weren’t understood. They hadn’t been assigned any function. They, too, could have been dismissed as “noise” or “junk.” But now hundreds of research scientists go to annual conferences to talk about these RNAs, and biotech companies are trying to use them to develop the next generation of pharmaceuticals. Certainly one lesson we’ve learned from the story of RNA is never to underestimate its power. Thus, these lncRNAs are likely to provide abundant material for future chapters in the book of RNA
Retarding Progress
Notice that the problem for Cech is not merely that he thinks the “junk RNA” hypothesis is false. The problem is that it is a presupposition that could be holding back scientific progress. After all, the scientists who (in Cech’s words) “do not share my enthusiasm for these RNAs” will not likely make discoveries about RNA that they think is junk. It’s scientists like Cech, who come to biology expecting plan and purpose, who will.
The implication of that is pretty significant: Darwinism is not turning out to be a fruitful heuristic for understanding genetics. (Since the lack of function in so-called “genetic dark-matter” is, of course, a prediction of the Darwinian model.) The trouble is, there isn’t another framework to take its place — well, not an acceptable one, anyway.
As far as I can tell, Cech assumes RNA will have function simply from experience, not from any underlying model or paradigm. RNA keeps turning out to have purpose, so he has learned to expect to find purpose. In contrast, other scientists don’t share his assumption because they (like Cech) are working in a paradigm that predicts junk, and (unlike Cech) they form their expectations based on that paradigm, not on the emerging pattern of evidence. Which is fair enough — it’s just a matter of how seriously you take your paradigm.
A New Paradigm
But if not taking a paradigm seriously turns out to be a path to scientific discovery, eventually you should start looking for a new paradigm. I would be interesting in hearing Dr. Cech’s answer to a question… Deep down, why do you really expect that genetic dark-matter has hidden functions? The neo-Darwinian paradigm didn’t predict that — what paradigm does?
Whatever his answer might be, it’s increasingly clear that the junk DNA narrative is over. Of course, some scientists still cling to it, but as they age out of the field it’s unlikely that many new researchers will inherit their assumption. The Darwinian prediction is being falsified. The older generation of scientists may not be ready to confront the implications of that. But the next generation will.
More primeval engineering vs. Darwin
Missiles and Jackhammers: How Plants Spread Themselves Far and Wide
On a new episode of ID the Future, I welcome science reporter David Coppedge to explore some fascinating examples of intelligent design in the plant world. Plants look so helpless tied to the soil, but they and fungi alike have perfected technologies for spreading themselves far and wide. Coppedge describes how various mechanisms, including cavitation and turgor pressure, enable these organisms to launch their spores effectively, turning them into short-range, medium-range, and even long-range missiles that travel great distances relative to their size in order to further life. The conversation also touches on the engineering principles behind plant root systems, and how studying these natural designs can inspire advancements in human technology through biomimetics.
You’ll learn about the fungi Deightoniella, for example, and how they use explosive bubble formation in their stalks to launch spores like tiny rockets as far as 15 times their own length. That might only be a few millimeters, but it’s enough to escape the boundary layer of still air on the leaf surface where they grow. Then there are ferns, which also use cavitation to create a miniature slingshot to shoot spores out at some of the fastest speeds in biology. And let’s not forget the mighty little fungus known as Pilobolus (pictured above), which uses turgor pressure like a mini squirt gun to shoot spores as far as six feet away!
Coppedge also discusses plant root systems, likening root tips to jackhammers and root hairs to stabilizers that allow plants to push through formidable barriers in search of nutrients and water. Coppedge explains how these plant systems exhibit irreducible complexity in their design and function. He also points out that by studying nature’s solutions to engineering problems, we can improve human engineering, an example of intelligent design in action. Download the podcast or listen to it here
Darwinism designs Darwinism?
The Convoluted Concept of Evolving Evolvability
Try to wrap your mind around the concept that evolvability evolves by natural selection. On second thought, don’t. It’s not conducive to mental health.
Valuing charity, I try to approach new evolutionary papers with dispassionate tolerance, seeking understanding before forming an opinion about them one way or another. This one was a particular challenge. It’s like trying to imagine a Mobius strip wrapping a Klein bottle in hyperspace. What on earth is meant by natural selection favoring the evolution of evolvability? Is this even a potentially useful notion for understanding how the world works?
Mentions of “evolvability” here at Evolution News can be found scattered through articles by several contributing authors, but none I searched for have treated it in detail. Now that two papers on evolvability have appeared in separate journals in February 2025, it’s a good time to examine the concept.
The first paper, in PNAS, led by Luis Zaman from the University of Michigan, will not require much analysis, for two reasons: (1) The authors are consumed with Darwinism to the point of absurdity, and (2) Their justification is entirely built on a computer model running Avida. Even the title of the press release mentions evolution five times! “Evolution, evolution, evolution: How evolution got so good at evolving.”
Now, a University of Michigan study shows that perhaps why evolution is so effective is that evolution is itself something that can evolve. The research is published in the Proceedings of the National Academy of Sciences.
“Life is really, really good at solving problems. If you look around, there’s so much diversity in life, and that all these things come from a common ancestor seems really surprising to me,” said Luis Zaman, an evolutionary biologist at U-M and lead author of the study. “Why is evolution so seemingly creative? It seems like maybe that ability is something that evolved itself.”
Forms of the word “evolution” appear 38 times in this short press release, and 214 times in the paper. Such overuse of a word appears pathological, like an addiction. Worse, it contains no biological field work at all. Its conclusions are rationalized entirely by a computer model with imaginary organisms in silico that were designed to evolve or fail by natural selection. Live Science liked the paper, but because the Avida platform that supported this computer game has been debunked extensively by others at Evolution News (here, here, and here), it deserves no further serious consideration other than for the possible entertainment value, like watching clowns in a curved maze looking for a penny in the nonexistent corner.
Much Empiricism About Nothing
The second paper, published in Science, gets more into the weeds. Barnett, Meister, and Rainey titled their work “Experimental evolution of evolvability.” For a synopsis of the paper, see the Perspective by Edo Kussell (“Enabling evolvability to evolve”) in the same issue of Science, or see the press release from the Max Planck Institute for Evolutionary Biology featuring two of the authors, Michael Barnett and Paul Rainey.
A new study by researchers at the Max Planck Institute for Evolutionary Biology (MPI-EB) sheds fresh light on one of the most debated concepts in biology: evolvability. The work provides the first experimental evidence showing how natural selection can shape genetic systems to enhance future capacity for evolution, challenging traditional perspectives on evolutionary processes.
Right at the outset, we see them “challenging traditional perspectives on evolutionary processes,” leading one to proceed with caution as if handed a bottle of New Coke. Arguing that mutation and selection interact, they propose a concept called “lineage-level selection.” Here we go; just what the world needs now: not love, sweet love, but another type of natural selection.
A caption to the opening diagram explains:
Central to this is lineage-level selection: bacterial lineages (connected nodes) were required to repeatedly evolve between two phenotypic states. Mutational transitions were initially unreliable, leading to lineage deathand replacement by more successful competitors. Final surviving lineages evolved mutation-prone sequencesin a key gene underpinning the phenotypes, enabling rapid transitions between states.
According to their concept, “natural selection optimises genetic systems for future adaptations.” Lineage selection locates the target of selection in the lineage rather than in the individual or population. In this view, your genealogy determines how natural selection will let you evolve.
Imaginary Foresight by Natural Selection
Dr. Marcos Eberlin wrote about Foresight as a sign of intelligence. In the theory of Barnett et al., however, foresight evolves (believe it or not). It’s not real foresight. It’s just imaginary foresight. They call it “evolutionary foresight.” Selection looks down through the halls of time and muses, “Which of my future lineages might win the competition for fitness?” It decides that the winner will be the most evolvable one. This is where the authors start playing mind games with your sanity. “This is not the selection you are looking for,” they say with a hypnotic gesture of the hands.
Evolution by natural selection is a blind process, but living systems can appear to possess evolutionary foresight. Mechanistically, this is conceivable. Certain configurations of gene regulatory networks, developmental systems, chromosomal architectures, and mutational processes have apparent adaptive utility in future environments. Taking advantage of such future adaptive potential requires not only memory of evolutionary history but often an ability to regenerate previously achieved phenotypic states. In this work, we show how selection on lineages can incorporate prior evolutionary history into the genetic architecture of a single cell, such that mutation appears to anticipate future environmental change.
They lost me on the assertion that “evolutionary foresight” is mechanistically conceivable. That is certainly not your grandpa’s Darwinism. At that point, I looked into their Materials and Methods to see what scientific experiments they did to support this notion. Sure enough, they ran actual lab experiments for three years on real organisms, not just computer models.
Madness in the Methodology
They carefully studied populations of the bacterium Pseudomonas fluorescens (pictured at the top) kept in “glass microcosms” (presumably flasks or test tubes) each with billions of cells. Some of the populations were able to manufacture cellulose (CEL+) and some were not (CEL–). When starved for oxygen, bacteria with the genes to make cellulose created cellulose mats on which individuals could get close to the air/liquid interface for access to oxygen. The presence of cellulose made by CEL+members, therefore, provided a fitness advantage (meaning, the ability to avoid dying).
The team identified “hypermutable” loci with 10,000 times the mutation rate that they describe as similar to “contingency loci” in pathogenic bacteria. Having a contingency plan sounds like design, but they believe the ability for rapid mutation gives the bacterium “foresight” in the form of “evolutionary potential.” The press release explains,
“Our findings show that selection at the level of lineages can drive the evolution of traits that enhance evolutionary potential, offering a fascinating glimpse into how evolution can gain what appears to be ‘foresight’.” Michael Barnett, the study’s first author, added: “By demonstrating the evolution of a hyper-mutable locus, we show that adaptation is not just about surviving in the present but also about refining the ability to adapt in the future.”
The results challenge the long-held view that evolution operates without foresight. Instead, they reveal how natural selection can embed evolutionary history into genetic architecture, enabling organisms to “anticipate” environmental changes and accelerate their adaptation.
Several design words can be seen there: architecture, anticipation, embedding. Are these things that blind selectors do? In a response to the paper, David G. King, emeritus professor from Southern Illinois University, saw something different going on: neither random mutation nor directed mutagenesis:
For example, the insertions and deletions that characterize short tandem repeats (and also enable phenotypic switching in bacterial contingency genes) confer “tuning knob” or “rheostat” functionality on many, perhaps most eukaryotic genes. Without being biased in the direction of adaptation, repeat number mutability helps assure a relatively advantageous distribution [of] mutation effects.
If so, this would indicate a function for such hypermutable loci. They act like “mutational sponges” that diffuse the harmful effects of random mutations. King explains,
This is the domain of “mutation protocols” whereby an abundant supply of unbiased mutations entails a minimal probability of harm. Put simply, mutations produced “according to protocol” are constrained to avoid vast domains of DNA sequence space where deleterious results would be practically guaranteed.
Design is evident in concepts like a “tuning knob” or “rheostat” functionality. Another idea not discussed in the paper is the possibility that the populations of bacteria form “quasispecies” in which members of a population retain functional loci that can be shared by horizontal gene transfer. In both cases, genetic changes would not be random.
Conceptual Flaws
But since the authors wish to argue that natural selection (NS), which they admit is “a blind process,” somehow had foresight to “enhance evolutionary potential” (i.e., evolvability), their convoluted concept is subject to the critical scrutiny of NS by illustrious writers including John West (“a corrosive impact on society”), Neil Thomas (“a conceptually incoherent term”), Jonathan Wells (“cannot explain the arrival of the fittest”), and others. Have Barnett et al. twisted NS into a creative force beyond its means by its very nature as an unguided process? Here are a few considerations to keep in mind:
No origin of species: They started with one species and ended with the same species.
Artificial selection: They acted like breeders, which is intelligent design, the opposite of NS.
Investigator interference: They forced the organisms to “evolve or perish” according to criteria they had set up in advance.
Unnatural assistance: When a population went “extinct” they transferred cells from a living population to keep it going (see the diagram in Kussell’s Perspective article).
Limited options: They forced the organisms to exhibit only one of two phenotypic states.
Personification: They applied terms like foresight, anticipation, and future adaptive potential to blind, mindless processes.
Magical thinking: Only in Darwin’s Fantasyland can NS be deemed capable of “refining the ability to adapt in the future.”
Obfuscation: Inventing concepts like “the evolution of evolvability” is no more conducive to understanding than speaking of “the phlogistification of phlogiston"
Conclusion: Keep Your Investment on Design
Try as they might to resurrect NS from the dead, Barnett et al. and Zaman et al. are stuck with blind, unguided processes with no foresight or desire to adapt. Scientists in Darwin’s day saw through his flawed attempt to present natural selection as analogous to artificial selection, as Robert Shedinger has exposed in Darwin’s Bluff.
Design scientists, by contrast, have the tools in their toolkit to explain adaptation. It takes foresight (real foresight by a designing intelligence, not imaginary “evolutionary” foresight) to engineer a machine for robustness against potential risks. More and more, scientists are finding that life comes equipped with built-in capabilities for adapting to environmental changes. This has been the focus of lively conferences on biological engineering over the past few years. The next Conference on Engineering in Living Systems (CELS), sponsored by Discovery Institute, is coming this summer in Seattle and promises to be a fertile occasion for enlightening discussions in Adventureland and Tomorrowland instead of Fantasyland.
Norway backs away from the brink(for now)
Court of Appeal Unanimously Overturns Unconstitutional Ruling in Norway
On March 14, 2025, the Borgarting Court of Appeal unanimously overturned the Oslo District Court’s decision to revoke the legal registration of JEHOVAH’S Witnesses in Norway. The Borgarting Court of Appeal also awarded our brothers 8,500,000 kroner ($806,833 U.S.) in compensation for legal costs incurred during both trials.
In 2022, the County Governor of Oslo and Viken revoked our registration, thereby blocking us from receiving State subsidies that more than 700 registered religious communities in Norway benefit from. The State based its decision on the assertion that we should change our Scriptural practice of removing unrepentant wrongdoers from the congregation. After the Oslo District Court upheld the government’s decision in March 2024, JEHOVAH’S Witnesses in Norway appealed. This latest decision overturns the lower court’s unconstitutional rulings. The State may still appeal this decision to the country’s Supreme Court.
During the appeal process, a panel of three judges thoroughly examined our religious practices and Bible-based teachings. In direct contradiction to the State’s claims, the Court of Appeal determined that limiting contact with an unrepentant wrongdoer who has been removed from the congregation is not a violation of his rights. In situations where an unrepentant baptized minor is removed from the congregation, the court ruled that it “does not constitute psychological violence.”
The court concluded that “JEHOVAH’S ’s Witnesses have been fully vindicated in that the decisions to deny grants and registration are invalid.”
We are pleased by the Court of Appeal’s decision in Norway, for which we give all thanks and praise to JEHOVAH.
How does JEHOVAH separate sinner from Sinner.
1John ch.5:16,17NLT"If you see a fellow believerd sinning in a way that does not lead to death, you should pray, and God will give that person life. But there is a sin that leads to death, and I am not saying you should pray for those who commit it. 17All wicked actions are sin, but not every sin leads to death."
The danger with the so called minor sins is that they are corrosive to the kind of character sincere Christians are attempting to cultivate,so the question is not whether this or that particular thought or act is disqualifying or not but whether this or that pattern of thinking and conduct causes me to more closely resemble my Savior and his God JEHOVAH or not. Every time we surrender to the flesh we become slightly weaker and every time we accept JEHOVAH'S Help and prevail over the flesh we become stronger and closer to our heavenly Father the Lord JEHOVAH,
But there is a class of sin that can't be tolerated by JEHOVAH or his true church, John says don't pray for those sinning in this way,
John ch.5:16"...But there is a sin that leads to death, and I am not saying you should pray for those who commit it."
Before there can be forgiveness there must come repentance and genuine repentance is not something that even JEHOVAH can impose on a sinner,
1Samuel Ch.16:1NLT"Now the LORD said to Samuel, “You have mourned long enough for Saul. I have rejected him as king of Israel, so fill your flask with olive oil and go to Bethlehem. Find a man named Jesse who lives there, for I have selected one of his sons to be my king.”"
It is always a cause for sadness when one who made a fine start turns away from his vow and starts living in obstinate and open defiance of JEHOVAH'S Law but JEHOVAH is telling us that barring some evidence of genuine repentance the time will come when we Must harden our hearts, JEHOVAH'S Cause will not suffer regardless of how many choose to abandon it,they will be replaced by determined loyalists who will bring glory to JEHOVAH
JEHOVAH'S true church is identified by a determination keep itself free of community guilt by not tolerating gross sin in its ranks and definitely not among its teachers.
1corinthians ch.5:12,13NIV"What business is it of mine to judge those outside the church? Are you not to judge those inside? 13God will judge those outside. “Expel the wicked person from among you.” d"
We are not sacralist who feel we have some mission to save the nation from itself through the installing of a Christian prince to impose God's law on the people.
We are the diplomatic mission of JEHOVAH'S Kingdom ,and we are eager to represent our sovereign in a worthy way,so we continually seek his unfailing help in remaining Holy individually and collectively
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