Darwinism schooled again by primeval tech.

Armed Forces in the Cell Keep DNA Healthy 

David Coppedge .

Science reporters struggle for metaphors to describe the complex operations they see going on in the cell. For example: 

The Orchestra 

News from the University of Geneva likens the human genome to a “complex orchestra.” Their research led to “unexpected” and “surprising” findings showing “harmonized and synergistic behavior” in the regulation of genes. The metaphor of a conductor keeping all the various players in harmony came to mind: 

A team of Swiss geneticists from the University of Geneva (UNIGE), the École Polytechnique Fédérale de Lausanne (EPFL), and the University of Lausanne (UNIL) discovered that genetic variation has the potential to affect the state of the genome at many, seemingly separated, positions and thus modulate gene activity, much like a conductor directing the performers of a musical ensemble to play in harmony. These unexpected results, published in Cell, reveal the versatility of genome regulation and offer insights into the way it is orchestrated 

The Armed Forces 

Another metaphor popular among reporters is “armed forces.” This metaphor will prove instructive as we read about DNA protection and damage repair. Let’s look at some of the stages in this process where we will find soldiers, emergency medical technicians, ambulances and military hospitals in action, each well trained and equipped for defense. 

Surveillance and Inspection 

Any disciplined military operation requires high standards. Soldiers at boot camp know that drill sergeants can be ruthless when inspecting rifles, shoe shines, and barrack beds. Similarly, machines in the genome inspect DNA for errors and won’t tolerate less than perfection. A news item from North Carolina State University describes MutS, a machine that inspects unzipped DNA strands looking for errors. Any mismatch makes this drill sergeant stop and stare the recruit in the face, even if he is one in a million. 

Fortunately, our bodies have a system for detecting and repairing these mismatches — a pair of proteins known as MutS and MutL. MutS slides along the newly created side of the DNA strand after it’s replicated, proofreading it. When it finds a mismatch, it locks into place at the site of the error and recruits MutL to come and join it. MutL puts a nick in the newly synthesized DNA strand to mark it as defective and signals a different protein to gobble up the portion of the DNA containing the error. Then the nucleotide matching starts over, filling the gap again. The entire process reduces replication errors around a thousand fold, serving as our body’s best defense against genetic mutations and the problems that can arise from them, like cancer. 

First Response 

If casualties occur, they have to be detected. A protein named ATF3 is captain of a squad that acts as “first responder” to DNA damage, as this from Georgia Regents University explains. Let’s say a DNA strand breaks because of sunlight, chemotherapy or a cosmic ray. If not corrected quickly, the cell could become cancerous or die. What happens first? 

In the rapid, complex scenario that enables a cell to repair DNA damage or die, ATF3, or activating transcription factor 3, appears to be a true first responder, increasing its levels then finding and binding to another protein, Tip60, which will ultimately help attract a swarm of other proteins to the damage site. 

Combat Operations 

Viruses have invaded! The armed forces go into high alert. The Salk Institute for Biological Studies describes the flurry of activities that result, because every organism “must protect its DNA at all costs.” 

Before panicking, the cell’s commanding officers need intelligence. If a DNA break puts the cell in stress, was it a natural break, let’s say from a cosmic ray, or from a virus, like an insurgent tossing a grenade? A false move could lead to friendly-fire casualties. 

The researchers explain how the cell figures out if the DNA damage was internal or external. First, the MRN complex gives the “all hands on deck” signal. It stops replication and other cell operations until the break is mended.  

What’s interesting is that even a single break transmits a global signal through the cell, halting cell division and growth,” says O’Shea. “This response prevents replication so the cell doesn’t pass on a break.” 

The viral response begins the same way, but doesn’t give the global alarm. Instead, the alarm is localized, and sentries in the area dispatch the invaders. There’s a reason for this. “If every incoming virus spurred a similarly strong response, points out O’Shea, our cells would be frequently paused, hampering our growth.” But when the cell becomes preoccupied with DNA damage repair, the viruses can infiltrate.

A video in the article applies the armed forces metaphor: 

Govind Shah: “DNA repair proteins serve as security guards inside the nucleus. They catch virus DNA and escort them out of the cell. If a cell experiences a huge amount of DNA damage, then these security guards will be pulled away from the viral DNA and allow the viral DNA to replicate to high levels.”

Clodagh O’Shea: “We discovered that if you have DNA damage in your own genome, and the alarm goes off, actually that recruits in all of the forces: all of the police, national guard–everyone’s there. All the forces are dealing with your own DNA damage, and there’s nothing left to actually even see or actually turn off the virus.” 

This gave them an idea. Shah says, “So why not use this to kill cancer cells” with viruses engineered to enter tumor cells? The programmed response they discovered will cause the cell to let the viruses in while it’s preoccupied with fixing DNA breaks. “If the cell can’t fix the DNA break, it will induce cell death-a self-destruct mechanism that helps to prevent mutated cells from replicating (and thus prevents tumor growth).”  

Medics 

We’re all familiar with the images of battlefield helicopters delivering medics to give first aid to the wounded, or airlifting them to the nearest triage station or hospital. The cell nucleus has hospitals, an article at Biotechniques says, and “A molecular ambulance for DNA” knows how to get the casualties to the emergency room. 

Double-strand breaks in DNA are a source of stress and sometimes death for cells. But the breaks can be fixed if they find their way to repair sites within the cell. In yeast, one of the main repair sites resides on the nuclear envelope where a set of proteins, including nuclear pore subcomplex Nup84, serves as a molecular hospital of sorts. The kinesin-14 motor protein complex, a “DNA ambulance,” moves the breaks to repair sites, according to a new study in Nature Communications. 

Researchers at the University of Toronto found it “very surprising” that the ambulance driver is the well-known motor protein kinesin-14 

Hospital Staff 

News from the University of Texas MD Anderson Cancer Center introduces some of the specialists in the DNA repair hospital: fumarase, a metabolic enzyme; DNA-PK, a protein kinase; and histone methylation enzymes that regulate the repair process. These skilled doctors perform restorative surgery for “DNA double-strand breaks (DSBs),” which “are the worst possible form of genetic malfunction that can cause cancer and resistance to therapy.” 

Clean-Up Crew 

Cells invest a lot of energy in their ribosomes, the organelles that translate DNA. Ribosomes are assembled from protein and RNA domains. What happens with the leftovers? An item from the University of Heidelberg describes molecular machines that barcode the fragments for delivery to a barrel-shaped shredder called the exosome. Though not described in military terms, the agents are under strict orders and required to pass through checkpoints. 

According to Prof. Hurt, the production of ribosomes is an extremely complex processthat follows a strict blueprint with numerous quality-control checkpoints. The protein factories are made of numerous ribosomal proteins (r-proteins) and ribosomal ribonucleic acid (rRNA). More than 200 helper proteins, known as ribosome biogenesis factors, are needed in the eukaryotic cells to correctly assemble the r-proteins and the different rRNAs. Three of the total of four different rRNAs are manufactured from a large precursor RNA. They need to be “trimmed” at specific points during the manufacturing process, and the superfluous pieces are discarded. “Because these processes are irreversible, a special check is needed,” explains Ed Hurt. 

The number of “armed forces” personnel involved in DNA defense and cell quality control is astonishing. It’s beyond a well-conducted orchestra. It’s like a military operation, with strict protocols, hierarchical command structure and trained specialists. These systems are goal-oriented: they exist to protect the genome. They are on duty inspecting components even when nothing is wrong. And when things do go wrong, they know just what to do, as if well-trained in following orders.

We aren’t surprised to notice that these articles say nothing about evolution. Why? Because we all know from our experience that phenomena characterized by hierarchical command and control systems with documented procedures and skilled agents are always intelligently designed. 

The new atheists: More Darwinian than Darwin?

 Darwin and the “New Atheists”  

Neil Thomas 

The somewhat superannuated 19th-century “conflict model” once used to define embattled evolutionary and religious claims to truth status has in our own time made an unheralded comeback in the writings of a diverse group of social commentators widely referred to as the “new atheists.”1 For much of the 20th century that older, conflict model, represented by the writings of the late Victorian era Andrew Dixon White2 and others, was modified in light of intellectual developments which came preponderantly to view science and religion as separate domains, each with its own sharply defined epistemological boundary.3 In the last few decades, however, some ideologically engaged scientific activists and commentators with erstwhile Oxford biologist Richard Dawkins at their head have seized the opportunity to weaponize Darwinism to push an atheist agenda against the backdrop of what they see as a dangerous uptick in global religious sentiment. In this and two subsequent posts I wish to explore how justified the group’s appropriation of Darwinian ideas is. 

Darwin’s Doubts 

ground zero as that advanced by Anaximander and his follower Anaximenes.5 And like the Greeks, Erasmus advanced no empirical evidence that would allow his claims to be tested. Not surprisingly then, evolution was widely regarded before 1859 as the minority preoccupation of a group of eccentrics rather than as a key to unlocking the mysteries of human existence.

Fast forward to a century later and we find that Charles Darwin was acutely aware of the checks and balances set up by modern science in order to establish any given theory as a demonstrable fact. Realizing that his grandfather’s ideas did not meet modern standards of proof, he looked for a sounder causal foundation for the Erasmian contribution to evolution. This he was to find in the theory of natural selection which he derived and developed from the writings of Thomas Malthus. It was via Malthus that Darwin thought to have discovered a mechanism or vera causa to underpin his grandfather’s ideas. In time, however, he began to harbor doubts about what he had first confidently hoped would be his game-changer with the capacity to bring evolutionary thought into a new era of acceptance and public prestige.

In later decades of his life, however, Charles began to doubt whether his postulated theory of natural selection would have been enough on its own to effect all the extraordinary transmutations evidenced by the world’s profusion of widely different species. This thought even led him to flirt with Lamarckian ideas of evolution which he had previously scorned.6

The upshot of the author’s second thoughts was that the sixth edition of the Origin was very different from the 1859 version and in some cases quite inconsistent with the first iteration of his ideas.7 Most strikingly, there arose within him a growing tension concerning his public postulation of an evolutionary theory dependent on natural selection and his claim in older age to be a “Theist” (Darwin’s own capitalization).8 It therefore appears that the more valid historical parallel for the new atheists is not Charles himself but Charles’s grandfather. The preoccupation of the Darwin family with evolutionary speculation was something which grew by stages9 and it is at a much earlier stage that a less ambiguous correlation emerges between evolutionary thought and atheism. 

Atheists Old and New 

What links Erasmus Darwin with the modern proponents of atheism is that the grandfather grew up against the background of that crypto-atheistical doctrine of deism according to which God had shrunk to the status of a deus absconditus or — to use the deprecatory contemporary cognomen — “absentee landlord.” Given such a backdrop of non-belief the question arises: Which came first in Erasmus’s thinking: the chicken or the egg? By which I mean: Was his desire to ponder possibilities of a purely material and naturalistic process of creation and evolution triggered by a deist conviction that, even if God had ever existed, he had now long since disappeared from human ken and was in that sense functionally irrelevant to human affairs? In other words, was his whole theory of evolution triggered by what is now called materialist confirmation bias (as one strongly suspects is the case of the new atheists)? For it is clear that if one has been convinced (or has convinced oneself) that there neither is nor can ever be evidence of divine direction in human affairs, then one is forced to speculate on some wholly material alternative, however illogical, impracticable, and physiologically improbable it might appear. 

Notes 

1)See The Four Horsemen: Dawkins, Dennet, Harris, Hitchens with a Foreword by Stephen Fry (London: Transworld/Penguin, 2019).

2)A History of the Warfare of Science with Theology in Christendom (New York: Appleton, 1896).

3)James Moore, The Post-Darwinian Controversies: A Study of the Protestant Struggle to Come to Terms with Darwin in Great Britain and America 1870-1900 (Cambridge: CUP, 1979). 

4)See renowned quantum mechanics specialist Carlo Rovelli’s The First Scientist: Anaximander and his Legacy (Yardley PA: Westholme, 2011).

5)See Erasmus Darwin, The Temple of Nature, facsimile of 1803 edition (Aldershot: Scolar Press, 1973), canto 1, ll. 295-315. 

6)Erasmus Darwin may have been first to put forward the suggestion of life having emerged from the depths of the oceans and evolving into different species in response to a striving for perfection in different environments. This was the somewhat simplistic (and erroneous) conception of physiological adaptation by sheer will-power he shared with Denis Diderot and the French biologist, Lamarck. 

7)See Peter J. Vorzimmer, Charles Darwin: The Years of Controversy: The Origin of Species and Its Critics 1859-1882 (London: London UP, 1972).

8)As Neal C. Gillespie once pointed out, Darwin was successful in banishing God from his science but not from his worldview. See his Charles Darwin and the Problem of Creation (Chicago: Chicago UP, 1979). 

9)The absolute origin of the Darwin family’s abiding preoccupation can be traced as far back as the year 1719 when Erasmus Darwin’s father, Robert, discovered the fossilized skeleton of a large part of a plesiosaur, described in the Philosophical Transactions of the Royal Society of that same year and now on display in the Natural History Museum in London. For Erasmus the finding of an extinct organism was taken as proof that species over long ages must undergo quite radical morphological change, and this inference was to lead him to develop his theory of common descent for the world’s animal types. See Charles Darwin’s The Life of Erasmus Darwin, edited by Desmond King-Hele (Cambridge: CUP, 2003), Introduction, p. xiii.  

Yet more on Darwinism place in the alt-wrong's master race delusions.

 Darwinian Racism, Past and Present 

Evolution News @DiscoveryCSC 

 

A new episode of ID the Future spotlights Darwinian racism, past and present. In this first half of a panel discussion at the 2022 Center for Science & Culture Insider’s Briefing, Darwin Day in America author John West introduces the other panel members, notes an upcoming book, Darwin Comes to Africa, and discusses his experience visiting the Museum of Criminal Anthropology (pictured above) in Turin, Italy, where the work of infamous Darwinian criminologist Cesare Lombroso’s racist ideas about evolution and race are on dramatic display. Then historian Richard Weikart, author of Darwinian Racism, debunks the popular media claim that white nationalist racism in America is a Southern evangelical phenomenon. Weikart shows that the most prominent white nationalists demonstrate little if any interest in promoting Christianity, but they very consistently anchor their racist ideas of white superiority and the racial struggle for supremacy in Darwinism, with straightforward links to Charles Darwin’s own ideas and arguments in The Descent of Man.

Weikart emphasizes that Darwinism does not necessarily lead its adherents to racism and, in fact, most Darwinists today are not racists. But racist ideas were woven into modern evolutionary thinking from the beginning and do serve as a major inspiration for white nationalist writers and even for some recent mass shooters. Weikart ends his lecture with a twist. He says there is one strongly anti-racist component in Darwinian materialism: such materialism, if true, means that all humans are equally without value — just so many DNA survival machines in a world without higher purpose or meaning. A grim takeaway, but only for those who feel compelled to embrace modern Darwinism. If you are open to questioning it, there are a wealth of resources here and at intelligentdesign.org showing that the evidence points strongly in another direction. Download the podcast or listen to it here.