Thursday 12 May 2022

The apostles creed.

Apostles’ Creed, also called Apostolicum, a statement of faith used in the Roman Catholic, Anglican, and many Protestant churches. It is not officially recognized in the Eastern Orthodox churches. According to tradition, it was composed by the 12 Apostles, but it actually developed from early interrogations of catechumens (persons receiving instructions in order to be baptized) by the bishop. An example of such interrogations used in Rome about 200 has been preserved in the Apostolic Tradition of Hippolytus. The bishop would ask, “Dost thou believe in God the Father almighty?” and so forth through the major Christian beliefs. Stated affirmatively, these statements became a creed; such creeds were known as baptismal creeds.

The present text of the Apostles’ Creed is similar to the baptismal creed used in the church in Rome in the 3rd and 4th centuries. It reached its final form in southwestern France in the late 6th or early 7th century. Gradually it replaced other baptismal creeds and was acknowledged as the official statement of faith of the entire Catholic church in the West by the time that Innocent III was pope (1198–1216). All creedal Protestant churches accept the Apostles’ Creed and use it in worship, but some (e.g., the United Methodist Church) delete the line “He descended to the dead.”

The accepted Latin version reads as follows:

Credo in Deum Patrem omnipotentem; Creatorem caeli et terrae. Et in Jesum Christum, Filium ejus unicum, Dominum nostrum; qui conceptus est de Spiritu Sancto, natus ex Maria virgine; passus sub Pontio Pilato, crucifixus, mortuus, et sepultus; descendit ad inferna; tertia die resurrexit a mortuis; ascendit ad caelos; sedet ad dexteram Dei Patris omnipotentis; inde venturus (est) judicare vivos et mortuos. Credo in Spiritum Sanctum; sanctam ecclesiam catholicam; sanctorum communionem; remissionem peccatorum; carnis resurrectionem; vitam aeternam. Amen.

A modern English version (as used in the Roman Catholic church) is the following:

I [We] believe in God, the Father almighty,

creator of heaven and earth.

I [We] believe in Jesus Christ, his only Son,

our Lord.

He was conceived by the power

of the Holy Spirit

and born of the Virgin Mary.

He suffered under Pontius Pilate,

was crucified, died, and was buried.

He descended to the dead.

On the third day he rose again.

He ascended into heaven,

and is seated at the right hand of the

Father.

He will come again to judge the living and

the dead.

I [We] believe in the Holy Spirit,

the holy Catholic Church,

the communion of saints,

the forgiveness of sins,

the resurrection of the body,

and the life everlasting. Amen.

The Nicene creed.

Nicene Creed, also called Niceno-Constantinopolitan Creed, a Christian statement of faith that is the only ecumenical creed because it is accepted as authoritative by the Roman Catholic, Eastern Orthodox, Anglican, and major Protestant churches. The Apostles’ and Athanasian creeds are accepted by some but not all of these churches.

Until the early 20th century, it was universally assumed that the Niceno-Constantinopolitan Creed (the more accurate term) was an enlarged version of the Creed of Nicaea, which was promulgated at the Council of Nicaea (325). It was further assumed that this enlargement had been carried out at the Council of Constantinople (381) with the object of bringing the Creed of Nicaea up to date in regard to heresies about the Incarnation and the Holy Spirit that had arisen since the Council of Nicaea.

Additional discoveries of documents in the 20th century, however, indicated that the situation was more complex, and the actual development of the Niceno-Constantinopolitan Creed has been the subject of scholarly dispute. Most likely it was issued by the Council of Constantinople, even though this fact was first explicitly stated at the Council of Chalcedon in 451. It was probably based on a baptismal creed already in existence, but it was an independent document and not an enlargement of the Creed of Nicaea.

The so-called Filioque clause (Latin filioque, “and the son”), inserted after the words “the Holy Spirit,…who proceeds from the Father,” was gradually introduced as part of the creed in the Western church, beginning in the 6th century. It was probably finally accepted by the papacy in the 11th century. It has been retained by the Roman Catholic, Anglican, and Protestant churches. The Eastern churches have always rejected it because they consider it a theological error and an unauthorized addition to a venerable document.

The Nicene Creed was originally written in Greek. Its principal liturgical use is in the context of the Eucharist in the West and in the context of both baptism and the Eucharist in the East. A modern English version of the text is as follows, with the Filioque clause in brackets:

I believe in one God,

the Father almighty,

maker of heaven and earth,

of all things visible and invisible.

I believe in one Lord Jesus Christ,

the Only Begotten Son of God,

born of the Father before all ages.

God from God, Light from Light,

true God from true God,

begotten, not made, consubstantial with the Father;

through him all things were made.

For us men and for our salvation

he came down from heaven,

and by the Holy Spirit was incarnate of the Virgin Mary,

and became man.

For our sake he was crucified under Pontius Pilate,

he suffered death and was buried,

and rose again on the third day

in accordance with the Scriptures.

He ascended into heaven

and is seated at the right hand of the Father.

He will come again in glory

to judge the living and the dead

and his kingdom will have no end.

I believe in the Holy Spirit, the Lord, the giver of life,

who proceeds from the Father [and the Son],

who with the Father and the Son is adored and glorified,

who has spoken through the prophets.

I believe in one, holy, catholic and apostolic Church.

I confess one Baptism for the forgiveness of sins

and I look forward to the resurrection of the dead

and the life of the world to come. Amen.

The Editors of Encyclopaedia Britannica This article was most recently revised and updated by Melissa Petruzzello.

Primeval tech continues to run up the score v. Darwinism

Transfer RNAs Wear Special Gear for Hot Water

David Coppedge

Thermophiles are bacteria and archaea that live in hot water. Some of these “extremophiles” thrive at temperatures right up to the boiling point. Ever since thermophiles gained attention decades ago, scientists have been intrigued at their specializations for surviving conditions that would kill most organisms. Because heat can quickly degrade biomolecules, those in thermophiles must be equipped with special survival gear.

The family of 20 canonical transfer RNAs (tRNAs) comprises the essential carrier of genetic information between DNA and protein. When charged by corresponding members of the family of aminoacyl-tRNA-synthetases (which know both the genetic code and the protein code), tRNAs connect amino acids together in the sequence specified by the messenger RNA. This takes place in the ribosome, the translation factory of the cell. That’s the simple story, but there’s more. Numerous modifications to tRNAs have been found in all cells — eukaryotes, bacteria, and archaea.

Writing in Nature, Ohira et al. from the University of Tokyo investigated how transfer RNAs in thermophiles beat the heat.

Thus far, about 150 types of RNA modification have been reported in various RNA molecules from all domains of life. In particular, tRNAs contain the widest variety and largest number of modified nucleosides, with 80% of RNA modifications identified in tRNA molecules. [Emphasis added.]

In their open-access paper, “Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance,” the authors found a unique modification that stabilizes tRNAs in archaea. And it’s reversible. After reviewing some of the RNA modifications that were previously known, they announced their discovery:

Here we report the identification of 2′-phosphouridine (U^p) in tRNAs, which, to our knowledge, is the first known instance of internal RNA phosphorylation. Biochemical, structural and genetic studies showed that U^p47 is a reversible RNA modification and confers thermal stability to tRNA, thereby contributing to cellular thermotolerance.

An Awesome Mod

This modification (we can call it a “mod” like the trendy word for add-ons in devices) is an unusual kind of kinase — an enzyme that spends ATP to attach a phosphate group to a substrate. U^p47 acts in an unusual spot on the tRNA; it “protrudes from the tRNA core and prevents backbone rotation during thermal denaturation.” Without this mod, the tRNA for valine would “melt” (fall apart) at around 65°C (149 °F); with it, the tRNA remained stable at 70°C (154 °F). “These observations clearly demonstrate that a single U^p47 modification increases the thermal stability of tRNA^Val3 by 6.6 °C.” In fact, it did not melt until 85 °C (185 °F).

Also of interest, this mod comes complete with a “writer” and “eraser” for adding and removing the stabilizer as needed. With this toolkit, the cell can fine-tune its adaptation to heat.

If U^p47 is a reversible modification, it is expected that tRNA function and stability are dynamically regulated by a writer and eraser, raising the possibility of epitranscriptomic regulation of tRNAs in translation. The mechanism closely resembles post-translational modification of proteins. Phosphorylation and dephosphorylation rapidly and dynamically control protein function. Because tRNA is a stable molecule with a low turnover rate and long lifetime in the cell, it would be reasonable for tRNA function to be regulated by U^p47 modification.

Writer and Eraser

The team identified the writer and eraser for this gadget named U^p47.

In addition, we identified the arkI gene, which encodes an archaeal RNA kinase responsible for U^p47 formation. Structural studies showed that ArkI has a non-canonical kinase motif surrounded by a positively charged patch for tRNA binding. A knockout strain of arkI grew slowly at high temperatures and exhibited a synthetic growth defect when a second tRNA-modifying enzyme was depleted. We also identified an archaeal homologue of KptA as an eraser that efficiently dephosphorylates Up47 in vitro and in vivo. Taken together, our findings show that U^p47 is a reversible RNA modification mediated by ArkI and KptA that fine-tunes the structural rigidity of tRNAs under extreme environmental conditions.

What does U^p47 look like? It stands for “2′-phosphouridine (U^p) at position 47 of tRNAs.” While phosphouridine is a fairly common biomolecule (a uracil nucleotide with a phosphate group attached; see diagram and info on PubChem), its specific targeting to spot 47 on the tRNA is essential to prevent thermal disruption. At that specific locus, it prevents the backbone from rotating, and stabilizes the correct angle of “puckering” in the ribose sugar.

Furthermore, no benefit would be incurred without the writer and eraser present in the correct quantities. How do they know when to act? The paper does not say when they become active. Presumably the stabilizer must be removed during translation or at other operational moments, but those times must be brief to prevent thermal damage.

Whether or not evolutionists can come up with a story of how this phosphouridine was recruited for its stabilizing role on tRNA, the specificity of its position and writer/eraser combo is remarkable. And it’s not the only required player the thermophile needs to survive in hot water. Another “mod” is found at position 54 in the T-loop of tRNAs. More are found in the anticodon loop at positions 34 and 37. Additional specialized “mods” have been found in other species. These authors are adding just one more to a pool of essential players in these thermophiles.

Origin Questions

Did these essential players evolve? At only one point do the authors mention evolution. Discussing mods to the V-loop in tRNAs, they say, “It is interesting that similar functions are evolutionarily conserved in different V-loop modifications across the domains of life.” That’s a statement about stasis, not evolution. As usual, evolution-talk is inversely proportional to the amount of detail presented about cellular workings.

To make matters worse, some evolutionists argue that thermophiles were the first organisms at the origin of life. One popular approach surmises that simple metabolic cycles began at hydrothermal vents, and then somehow became incorporated within primitive membranes. This compounds their hassles, because additional “gear” for thermal stabilization would have been needed right at the time they imagine primitive cells were trying to emerge. It also tosses the difficult problem of the origin of genetic coding to someone else to figure out.

For the Awe of It

Visitors by the millions walk by the hot springs of Yellowstone, unaware of the complex systems at work in the colorful runoff channels where these thermophiles live. Even if readers of Evolution News don’t wish to memorize the details in this article, it’s good for the soul to gain an appreciation for the real specified complexity at work in even the most “primitive” of life forms. It encourages awe of nature, which psychologists recognize as a healthy attitude (see video by Science with Sam). So don’t worry about remembering U^p47. If your awe rose a few degrees while reading this, it was worth it.

Anecdote in closing: it was through the study of thermophiles in Yellowstone hot springs that biochemists discovered the enzyme “taq polymerase.” Subsequent study of this enzyme revealed that it can amplify DNA at high temperatures. This led to the lab technique called polymerase chain reaction (PCR), a method that made possible the rapid amplification of biomolecules for research and essentially started the biotechnology revolution. PCR was even essential during the development of vaccines and therapeutics for COVID-19. For the awe-inspiring story, see an article at USGS.

Sanction proofed?

Following the science re: Human life.

If a Fetus Isn’t a Human Being, What Is It?

Michael Egnor

At the heart of the abortion debate are two sets of questions: scientific questions and moral questions. They are both important, and much of the rancor and division in the abortion debate stems, I think, from conflation of scientific and moral issues. They are not the same. Properly formed moral views depend on correct scientific understanding. If we don’t know what a fetus is, scientifically, we are hampered in making sound moral judgments about its protection.

A recent post by biologist Jerry Coyne exemplifies this confusion. Coyne asks:

Where, I ask, is the evidence (beyond that asserted by religious authorities) that abortion is identical to murder, even in its very early stages? There is clearly a developmental continuum in a fetus, with an abrupt break when the baby is born, and so drawing a line for when a fetus becomes equivalent to a person with rights, including freedom from “murder”, is purely arbitrary. Many Catholics, though, draw the line at a rationally insupportable stage: fertilization. A “person” is not created at fertilization: we have a zygote that now will go on to continue development. That zygote is an undifferentiated ball of cells without mentation or the ability to feel pain. And there’s no evidence it has a soul or anything differentiating it from the embryos of any number of vertebrate species.

Coyne profoundly misunderstands the biology of human development, and in doing so he reaches moral conclusions that even he — if he were to have a clear view of the science — would be hard-pressed to defend. How is it that a leading professor of biology could fundamentally misunderstand the biology of human development?

Let Me Explain

Let us restrict our question about the nature of the fetus to the science of human development in the womb, which has been understood reasonably well since the mid 19th century. The question at issue is this: When does human life begin? Note that we are not asking moral questions or even metaphysical questions per se. We’re asking about biology: when, from a biological perspective, does an individual human being first exist?

We all agree that life begins at or after union of the sperm and egg. Fertilization marks the earliest moment in human development that human life might begin. Many other times after fertilization have been proposed — the first appearance of nervous tissue, or heartbeat, or brain waves, or quickening, or the ability to feel pain, or viability outside of the womb, or birth, or rationality, etc. At first, it seems a hopeless conundrum: there seem to be so many possible moments at which life begins that science is stymied. Perhaps science can’t tell us when life begins. But science most certainly can tell us, and does tell us.

Every living cell or group of cells is either an individual member of a species or a part of an individual member of a species. There are no unclassified living things. And we all agree (tautologically) that whenever human life begins, each human life after that point is a member of the species Homo sapiens. But of course that entails a corresponding and critical question: What is the tissue (zygote, embryo, fetus, or neonate) before it is an individual human being?

The Critical Scientific Issue

So the critical scientific issue at the heart of the question “when does human life begin” is: What scientific description of the tissue (let’s call it the “fetus” for brevity) before human life begins makes sense biologically? Consider the options:

The fetus is a part of the mother’s body.
The fetus is not part of the mother’s body, but is an individual of another species.
The fetus is not any kind of living thing — it’s just a clump of biological molecules undergoing chemical reactions.

Consider the scientific implications of each option:

1) The fetus is a part of the mother’s body. if the fetus is a part of the mother’s body, then all pregnant women are chromosomal mosaics. That is, they are organisms that have two sets of genomes. Chromosome mosaicism is a rare disorder and is not synonymous with pregnancy. There is no such thing as “transient chromosomal mosaicism.” Furthermore, if the fetus is a part of the mother’s body, then half of pregnant women are hermaphrodites — i.e., they contain both male and female tissues. Needless to say, “transient gestational hermaphroditism” is not a recognized medical disorder.

Furthermore, if a new human life begins by a piece of the mother’s body becoming a new organism, then human beings reproduce by budding. Budding is a form of asexual reproduction used by some species of worms, sponges, corals, and microorganisms, but it is not a means of human reproduction.

There is no biological sense to be made of the claim that “the fetus is part of the mother’s body.” The claim leads to scientific implications that are nonsense.

2) The fetus is not part of the mother’s body but is an individual of another species. If the fetus is an individual member of another species, then pregnancy is by far the most common parasitic disease among humans. What’s more, the transition in each pregnancy from a non-human parasite to a new human being is speciation — the evolution of a new species, “Homo fetus” to Homo sapiens — occurring with each pregnancy. This is, of course, scientific nonsense.

3) The fetus is not any kind of living thing — it’s just a clump of biological molecules undergoing chemical reactions. If the fetus is not really living at all, then each pregnancy is a new origin-of-life event. This is also scientific nonsense.

Clear and Straightforward Science

So the biological answer to the question “When does human life begin?” is easy to answer from a scientific perspective: human life begins at the moment the sperm fertilizes the egg. This is not merely common sense and the claim of pro-life advocates, it is clear and straightforward science, as settled as heliocentrism and the existence of atoms.

All cogent moral reasoning about abortion must begin with the understanding that human life begins at fertilization. There are no other scientific options. And here you can see where Coyne and other abortion proponents — even abortion proponents who are scientists — go awry. They don’t understand the simplest biological fact about human development — that human life begins at fertilization.

So Coyne’s assertion…

A “person” is not created at fertilization: we have a zygote that now will go on to continue development. That zygote is an undifferentiated ball of cells without mentation or the ability to feel pain. And there’s no evidence it has a soul or anything differentiating it from the embryos of any number of vertebrate species.

…is nonsensical because it confuses scientific misunderstanding with moral reasoning.

There is a simple scientific answer to the basic question at the heart of the abortion debate. Whatever a “person” is, a human zygote is most certainly a human being.

The term “person” is a moral and legal category, not a scientific category, and it is a category open to moral discussion and debate. But “human being” is a scientific term, and it is not open to debate. The science is settled. Human life begins at fertilization, and cogent moral reasoning about abortion must begin with that scientific fact.

Man reprivileged again? II

How We Moved Beyond Darwin to the Miracle of Man

Michael Denton

Summary: Even as the scientific vision of humankind as an accidental by-product of the cosmos became ascendant, the first seeds of a new scientific revolution were sprouting, one revealing the fine-tuning of nature for human existence.

Editor’s note: This week sees the release of biologist Michael Denton’s new book The Miracle of Man: The Fine-Tuning of Nature for Human Existence. This essay is adapted from the opening chapter of Denton’s new book.

With the acceptance of Darwinism by the biological mainstream, Western civilization took the final step back to the atomism, materialism, and many-worlds doctrine of Democritus and other pre-Socratic philosophers of ancient Greece. As the Darwinian paradigm tightened its grip on mainstream biology and science, all vestiges of the old teleological-organismic universe, all notions which placed humankind or life on Earth in any special or privileged place in the order of things, were banished from mainstream academic debate.

The implications of the final Darwinian unraveling for mainstream evolutionary biologists was memorably captured by French biochemist Jacques Monod in his materialist manifesto Chance and Necessity. “The thesis I shall present in this book is that the biosphere does not contain a predictable class of objects or of events,” he wrote, “but constitutes a particular occurrence, compatible indeed with first principles, but not deducible from those principles and therefore essentially unpredictable… unpredictable for the same reason — neither more nor less — that the particular configuration of atoms constituting this pebble I have in my hand is unpredictable.”

According to Monod the human race was adrift in an uncaring cosmos which knew nothing of its becoming or fate, an infinite universe said to manifest not the slightest evidence of anthropocentric bias. Instead, as Harvard paleontologist Stephen Jay Gould put it, we are merely “the embodiment of contingency,” our species but “a tiny twig on an improbable branch of a contingent limb on a fortunate tree… we are a detail, not a purpose… in a vast universe, a wildly improbable evolutionary event.” Or as astronomer Carl Sagan framed the matter, “one voice in the cosmic fugue.”

Demoted to an Epiphenomenon

Thus was humanity demoted to a mere epiphenomenon, to one un-purposed by-product among many, from the imago Dei as understood in the medieval vision of humanity — that of a being made in the image of God and pre-ordained from the beginning — to a meaningless contingency, something less than a cosmic afterthought.

This modern secular vision of nature is as far removed from the anthropocentric cosmos of the medieval scholastic philosophers as could be imagined, representing one of the most dramatic intellectual transformations in the history of human thought.

But a funny thing happened on the way to the 21st century.

A Second Revolution

Even as the scientific vision of humankind as an accidental by-product of the cosmos consolidated its position of ascendancy in Western thought, the first seeds of a new scientific anthropocentricism were sprouting, in the Bridgewater Treatises of the 1830s. The multivolume work included such contributions as William Whewell’s discussion of the striking fitness of water for life and William Prout’s discussion of the special properties of the carbon atom for life, revealed by the development of organic chemistry in the first quarter of the 19th century. And ironically it was during the decades following the publication of The Origin of Species (1859), during the very period when Friedrich Nietzsche proclaimed that “nihilism stands at the door,” when fresh scientific evidence began to accumulate suggesting that life on Earth might after all be a special phenomenon “built into” the natural order and very far from the accident of deep time and chance that the Darwinian materialist zeitgeist assumed.

Two Pivotal Books

These discoveries, and particularly the unique chemistry of carbon, were explored in World of Life by none less than the co-discover with Charles Darwin of evolution by natural selection, Alfred Russel Wallace. In that 1911 work, Wallace showed that the natural environment gave various compelling indications of having been pre-arranged for carbon-based life as it occurs on Earth.

Two years later, in 1913, Lawrence Henderson published his classic The Fitness of the Environment, whichpresented basically the same argument but in much more scholarly detail. Henderson not only argued that the natural environment was peculiarly fit for carbon-based life but also in certain intriguing ways for beings of our physiological design. He refers to two of the thermal properties of water, its specific heat and the cooling effect of evaporation, as well as the gaseous nature of CO₂ as special elements of environmental fitness in nature for beings of our biological design.

Building on the evidence alluded to by Wallace and Henderson, other more recent scholars, including George Wald and Harold Morowitz, have further defended the fitness paradigm during the 20th century. Wald argued for the unique environmental fitness of nature for carbon chemistry and photosynthesis. Morowitz argued for the unique fitness of water for cellular energetics.

These discoveries signal a sea change. In my new book, The Miracle of Man, I provide what is to my knowledge the most comprehensive review in print of nature’s unique fitness for human biology by describing a stunning set of ensembles of prior environmental fitness, many clearly written into the laws of nature from the moment of creation, enabling the actualization of key defining attributes of our biology. The evidence puts to bed the notions of Gould, Monod, and Sagan that humankind is a mere contingent outcome of blind, purposeless, natural processes.

Controversial and Outrageous?

I agree that to claim that the findings of modern science support a contemporary take on the traditional anthropocentric worldview is highly controversial and will seem outrageous to many commentators and critics. Here a distinction may prove useful. While my conclusions are controversial, the evidences upon which they are based are not in the least controversial. In virtually every case they are so firmly established in the relevant scientific disciplines as to now be considered wholly uncontroversial conventional wisdom. In other words, the extraordinary ensembles of natural environmental fitness described in my book, ensembles vital for our existence and upon which my defense of the anthropocentric conception of nature is based, are thoroughly documented scientific facts. What is unique here is the comprehensive integration of so many disparate, if overlapping, ensembles of fitness. And when we step back from these individual groves and take in the proverbial forest in all its grandeur, the panorama, I would go so far as to say, is overwhelming.

In The Miracle of the Cell I showed that the properties of many of the atoms of the periodic table (about twenty) manifest a unique prior fitness to serve highly specific and vital biochemical roles in the familiar carbon-based cell, the basic unit of all life on Earth. And as I stressed, it was the prior fitness of these atoms for specific biochemical functions which enabled the actualization of the first carbon-based cell irrespective of whatever cause or causes were responsible for its initial assembly. Now the focus turns to beings of our physiological and anatomical design and the numerous ensembles of environmental prior fitness necessary for our existence. This is a prior fitness that existed long before our species first appeared on planet Earth, a fitness that led the distinguished astrophysicist Freeman Dyson to famously confess, “I do not feel like an alien in this universe. The more I examine the universe and study the details of its architecture, the more evidence I find that the universe in some sense must have known that we were coming.”

And it is not only our biological design which was mysteriously foreseen in the fabric of nature. As The Miracle of Man shows, nature was also strikingly prearranged, as it were, for our unique technological journey from fire making, to metallurgy, to the advanced technology of our current civilization. Long before man made the first fire, long before the first metal was smelted from its ore, nature was already prepared and fit for our technological journey from the Stone Age to the present.

Hype v. reality re: OOL science

Did U of Tokyo Just Solve the Mystery of Life’s Origin?

Evolution News @DiscoveryCSC

On a new episode of ID the Future, Brian Miller, research coordinator for the Center for Science & Culture, reports on laboratory research recently presented in Nature Communications and in a University of Tokyo press release — research that supposedly provides dramatic “new insights into the possible origin of life,” and specifically “the molecular evolution of RNA.” The media picked up on these claims and ran with them, including in a Quanta article that breathlessly reported, “When researchers gave a genetic molecule the ability to replicate, it evolved over time into a complex network of ‘hosts’ and ‘parasites’ that both competed and cooperated to survive.”

Miller says nothing remotely this dramatic occurred in the experiment. He explains that there were no great revelations from this laboratory work, aside perhaps from its further corroborating the view that precisely orchestrated interventions of an intelligent designer (in this case, that of the lab researchers) are required in order to make any headway on the road from non-life to life.

But as Miller’s conversation with host Eric Anderson suggests, even that might be to exaggerate what the University of Tokyo experimenters accomplished, since the RNA “evolution” they achieved was actually devolution. Download the podcast or listen to it here. And for more, check out Miller’s Evolution News article on the subject.

Man reprivileged again?

The Miracle of Man: New Book by Michael Denton

David Klinghoffer

“The wheel has turned,” writes biologist Michael Denton in his new book, out today, The Miracle of Man. A widening divorce that originated in the 16th century between our understanding of man and of the cosmos has been healed by discoveries in modern science. That is, if we’re willing to recognize it.

From the heliocentric revolution of Nicolaus Copernicus in 1543, to Darwin’s Origin of Species in 1859, science demoted man further and further, to the status of an afterthought in the cosmic scheme. Or not even an “afterthought.” As it seemed, neither life nor the universe gave evidence of a thinking designer. Rather than reflecting cosmic purpose, man was evidently of no consequence. This thought had profound consequences for Western culture. In 1901, with the science of his day in mind, Nietzsche could write that “nihilism stands at the door.” That, however, was about to change.

Downfall and Recovery

In 1911 and 1913, two pivotal years, there appeared books by Alfred Russell Wallace (co-discoverer of evolution by natural selection) and Harvard chemist Lawrence Henderson. In their work, the extraordinary fine-tuning of chemistry and physics was starting to come into focus. As it advanced, science delivered the news that from the outset of physical existence, at the Big Bang, the universe had planned for a miracle. And the miracle came. It was the rise of our human species in the Pleistocene epoch, proceeding from the use of stone tools to fire to metalworking, giving us, ultimately, our modern world.

For this, a vast suite of chemical and physical parameters were precisely set. These parameters are “uniquely fit” for creatures like ourselves, as Denton shows:

[O]ur existence as energy-demanding active air-breathing terrestrial organisms critically depends on a wildly improbable ensemble of natural environmental fitness comprising various chemical and physical laws as well as the properties of specific molecules such as oxygen and CO₂ and specific elements such as the transition metals, properties that must be almost exactly as they are.

The cosmic and planetary environments, in other words — the hydrological cycle, the atmosphere, water, oxygen, and more — were designed with us in mind — our breathing, circulation, vision, muscles, nerves, brain, bones, and much else.

“A Primal Blueprint”

Both lyrical and soberly detailed, Denton writes,

The exquisitely fine-tuned ensembles of environmental fitness described here, each enabling a vital aspect of our physiological design, amount to nothing less than a primal blueprint for our being, written into the fabric of reality since the moment of creation, providing compelling evidence that we do indeed, after all, occupy a central place in the great cosmic drama of being.
This is the miracle of man. We are not positioned in the spatial center of the universe as was believed before Copernicus, but what we have found over the past two centuries confirms the deep intuition of the medieval Christian scholars who believed that “in the cognition of nature in all her depths, man finds himself.”

The Miracle of Man takes a story of downfall and recovery full circle. And it does so in a fascinatingly similar way to the story told by Denton’s Discovery Institute colleague, philosopher of science Stephen Meyer, in his recent book Return of the God Hypothesis. The evidences discussed by Denton and by Meyer are quite different. But they point to the same conclusion. This is so much so that Denton’s book could accurately, but not mellifluously, have been titled Return of the Anthropocentric Hypothesis.

True but Trivial

Of course, there’s a ready objection. Since humans find ourselves in existence, we must be fit for our environment. This is obviously true, says Denton. But it’s “trivial.” The remarkable observation is just how precisely the environment was specified for us. That is not trivial at all. It is a mark of supreme privilege.

From Denton’s superb presentation, other conclusions follow. For one, if the universe harbors intelligent extraterrestrials, they will not be “aliens” to us. Instead, because of the cosmic design, they will “strongly resemble Homo sapiens.” Their planet, or planets, will resemble our own, for the same reason. If they find a way to visit us, as UFO believers say, they will feel that they have come home.

The book culminates the series of works in Dr. Denton’s Privileged Species series. And it arrives, I have to add, in a strangely providential manner. In the United States, sputtering nihilists and screaming anarchists have turned their rage on the idea that someone, somewhere, could be thinking that the unborn man or woman is a miracle worth protecting. This is a consequential book — and, as the editors could not have predicted, a timely one.

On the new gods and the alt-wrong.

Anti-Racists Often Ignore This Non-Religious Source of Racism

Richard Weikart

Scholars today are cranking out multitudes of books exposing the racism in our society. Three prominent examples from 2021 — published by academic presses — are Anthea Butler, White Evangelical Racism, Randall Balmer, Bad Faith: Race and the Rise of the Religious Right, and J. Russell Hawkins, The Bible Told Them So: How Southern Evangelicals Fought to Preserve White Supremacy. One can hear a similar refrain on NPR: for example, in the July 2020 report, “White Supremacist Ideas Have Historical Roots in U.S. Christianity” or in many reports during 2021 warning about white supremacism inherent in “Christian nationalism.”

While it is salutary to examine and expose the religious roots of racism, one might get the mistaken impression from this discourse that today’s white nationalists are direct heirs of the Ku Klux Klan, who did indeed (mis)use religion to promote their racist ideology.

The Real Roots of Racism: Pseudo-Science

What often seems neglected in this discussion is the history of scientific racism, which was in some ways more virulent than most religious forms of racism. This is not to say that historians have completely ignored scientific racism. Indeed, I have contributed to this scholarly discussion in some of my earlier works, as well as in my recently released book, Darwinian Racism: How Darwinism Influenced Hitler, Nazism, and White Nationalism.

However, it seems that the way scientific racism is presented differs substantially from the way religious racism is treated. Many scholarly works and NPR stories on religious racism assume that religion — especially evangelical Christianity — is still heavily tainted by racism. Indeed, an op-ed in Scientific American in 2021, “Denial of Evolution Is a Form of White Supremacy,” overtly slammed creationists as white supremacists, completely ignoring the fact that Ken Ham, a leader among young-earth creationists, co-authored a book (with an African American), in which he vigorously opposes racism.

Most works on scientific racism admit that scientists erred in the past by promoting racist ideas, but then the historians celebrate the triumph of science, since later scientists overcame these misguided ideas. Of course, most scientists today — just as most religious leaders today — do reject racism. One of the outliers — Nobel-Prize-winning biologist James Watson — is often condemned by colleagues when he makes racist statements.

The Eugenicist in the Room

So, if the vast majority of scientists reject racism, one might conclude that scientific racism is no longer a problem. Maybe religious racism really is a more important target. However, this conclusion ignores the elephant in the room.

What elephant? Well, how about examining the white nationalist scene today to see what they actually believe? How do they justify their racist ideology? While researching my book, Darwinian Racism, I examined the websites and publications of many neo-Nazi, white nationalist, and alt-right individuals and organizations. What I discovered was that most white nationalists and white supremacists today embrace a social Darwinist version of scientific racism and vehemently oppose Christianity.

Might Is Right

One of the most virulent pieces of social Darwinist racism I have ever read is the 1896 book Might Is Right by Ragnar Redbeard (a pseudonym), which is currently popular among white supremacists. Indeed, in 2019, shortly before a 19-year-old gunman at the Gilroy Garlic Festival killed three and wounded 17, he recommended on social media that people read Redbeard’s book.

Many white nationalist websites recommend this book, and some even sell it. The subtitle of Redbeard’s book is Survival of the Fittest, and it is laced with Darwinian themes, such as the inescapable necessity of a struggle for existence between races. In addition to demeaning non-white races, Redbeard’s book also vociferously attacks Christianity.

The Survival of the Fittest … Race

Many white nationalists claim that Darwinism directly supports their ideology, because they think that races have evolved to different levels. They are convinced that races are pitted in a merciless struggle for existence. Their penchant for white supremacy is their bid to win the Darwinian struggle for existence.

Those doing battle against the religious roots of racism do often uncover vestiges of racism and this can be helpful. However, sometimes they seem to be letting the most flagrant proponents of racism off the hook. Could it be that they are uncomfortable recognizing that most white nationalists today are thoroughly secular and are inspired by Darwinism and science, rather than religion?

This article was originally published at Townhall.

Monday 9 May 2022

(As always the question is) Who will watch the watchers?

The Caesars of 1st century.

1st century ce

Augustus (31 bce–14 ce)
Tiberius (14–37 ce)
Caligula (37–41 ce)
Claudius (41–54 ce)
Nero (54–68 ce)
Galba (68–69 ce)
Otho (January–April 69 ce)
Aulus Vitellius (July–December 69 ce)
Vespasian (69–79 ce)
Titus (79–81 ce)
Domitian (81–96 ce)
Nerva (96–98 ce)

But who will save us from our friends?

Actual design: A science stopper?

Science Stopper? Intelligent Design as a Fruitful Scientific Paradigm

Casey Luskin

Editor’s note: We have been delighted to present a series by geologist Casey Luskin on “The Positive Case for Intelligent Design.” This is the 12^th and final entry in the series, a modified excerpt from the new book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. Find the full series here.

There’s a final common objection to intelligent design that the positive case for ID, outlined in this series, helps us to answer. In his Kitzmiller v. Dover testimony, biologist Kenneth Miller referred to intelligent design as a “science stopper.”¹ Similarly, in his book Only a Theory, Miller stated, “The hypothesis of design is compatible with any conceivable data, makes no testable predictions, and suggests no new avenues for research. As such, it’s a literal dead end…”²

Yet as we’ve already seen, ID makes a variety of testable and successful predictions. This allows ID to serve as a paradigm guiding scientific research to make new discoveries. The list below shows various fields where ID is helping science to generate knowledge. For each field, multiple ID-friendly scientific publications are cited as examples.

How ID Inspires the Progress of Science

Protein science: ID encourages scientists to do research to test for high levels of complex and specified information in biology in the form of the fine-tuning of protein sequences.³ This has practical implications not just for explaining biological origins, but also for engineering enzymes and anticipating and fighting the future evolution of diseases.
Physics and cosmology: ID has inspired scientists to seek and find instances of fine-tuning of the laws and constants of physics to allow for life, leading to new fine-tuning arguments such as the Galactic Habitable Zone. This has implications for proper cosmological models of the universe, hinting at proper avenues for successful “theories of everything” that must accommodate fine-tuning, and other implications for theoretical physics.⁴
Information theory: ID leads scientists to understand intelligence as a cause of biological complexity, capable of being scientifically studied, and to understand the types of information it generates.⁵
Pharmacology: ID directs both experimental and theoretical research to investigate the limitations of Darwinian evolution to produce traits that require multiple mutations in order to function. This has practical implications for fighting problems like antibiotic resistance or engineering bacteria.⁶
Evolutionary computation: ID produces theoretical research into the information-generative powers of Darwinian searches, leading to the discovery that the search abilities of Darwinian processes are limited, which has practical implications for the viability of using genetic algorithms to solve problems.⁷
Anatomy and physiology: ID predicts function for allegedly “vestigial” organs, structures, or systems whereas evolution has made many faulty predictions of nonfunction.⁸
Bioinformatics: ID has helped scientists develop proper measures of biological information, leading to concepts like complex and specified information or functional sequence complexity. This allows us to better quantify complexity and understand what features are, or are not, within the reach of Darwinian evolution.⁹
Molecular machines: ID encourages scientists to reverse-engineer molecular machines — like the bacterial flagellum — to understand their function like machines, and to understand how the machine-like properties of life allow biological systems to function.¹⁰
Cell biology: ID causes scientists to view cellular components as “designed structures rather than accidental by-products of neo-Darwinian evolution,” allowing scientists to propose testable hypotheses about cellular function and causes of cancer.¹¹
Systematics: ID helps scientists explain the cause of the widespread features of conflicting phylogenetic trees and “convergent evolution” by producing models where parts can be reused in non-treelike patterns.¹² ID has spawned ideas about life being front-loaded with information such that it is designed to evolve, and has led scientists to expect (and now find!) previously unanticipated “out-of-place” genes in various taxa.¹³
Paleontology: ID allows scientists to understand and predict patterns in the fossil record, showing explosions of biodiversity (as well as mass extinction) in the history of life.¹⁴
Genetics: ID has inspired scientists to investigate the computer-like properties of DNA and the genome in the hopes of better understanding genetics and the origin of biological systems.¹⁵ ID has also inspired scientists to seek function for noncoding junk-DNA, allowing us to understand development and cellular biology.¹⁶

Avenues of Discovery

Critics wrongly charge that ID is just a negative argument against evolution, that ID makes no predictions, that it is a “god of the gaps” argument from ignorance, or that appealing to an intelligent cause means “giving up” or “stopping science.” As this series has shown, these charges are misguided.

Ironically, when critics claim that research is not permitted to detect design because that would stop science, it is they who hold science back by preventing scientists from investigating the scientific theory of intelligent design. When researchers are allowed to infer intelligent agency as the best explanation for information-rich structures in nature, this opens up many avenues of discovery that are bearing good fruit in the scientific community.

Notes

Kenneth R. Miller, Kitzmiller v. Dover, Day 2 AM Testimony (September 27, 2005).
Kenneth R. Miller, Only a Theory: Evolution and the Battle for America’s Soul (New York: Viking Penguin, 2008), 87.
Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors”; Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds”; Behe and Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues”; Axe, “The Case Against a Darwinian Origin of Protein Folds”; Gauger and Axe, “The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway”; Reeves et al., “Enzyme Families-Shared Evolutionary History or Shared Design? A Study of the GABA-Aminotransferase Family”; Thorvaldsen and Hössjer, “Using statistical methods to model the fine-tuning of molecular machines and systems.”
Guillermo Gonzalez and Donald Brownlee, “The Galactic Habitable Zone: Galactic Chemical Evolution,” Icarus 152 (2001), 185-200; Guillermo Gonzalez, Donald Brownlee, and Peter D. Ward, “Refuges for Life in a Hostile Universe,” Scientific American (2001), 62-67; Guillermo Gonzalez and Jay Wesley Richards, The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery (Washington, DC, Regnery, 2004); Guillermo Gonzalez, “Setting the Stage for Habitable Planets,” Life 4 (2014), 34-65; D. Halsmer, J. Asper, N. Roman, and T. Todd, “The Coherence of an Engineered World,” International Journal of Design & Nature and Ecodynamics 4 (2009), 47-65.
William A. Dembski, The Design Inference; William A. Dembski and Robert J. Marks II, “Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search,” Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics(October 2009), 2647-2652; William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search,” Journal of Advanced Computational Intelligence and Intelligent Informatics 14 (2010), 475-486; Øyvind Albert Voie, “Biological function and the genetic code are interdependent,” Chaos, Solitons and Fractals 28 (2006), 1000-1004; McIntosh, “Information and Entropy —Top-Down or Bottom-Up Development in Living Systems?”
Behe and Snoke, “Simulating evolution by gene duplication of protein features that require multiple amino acid residues”; Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke, “Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,” BIO-Complexity 2010 (2).
William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success,” IEEE Transactions on Systems, Man, and Cybernetics-Part A: Systems and Humans 39 (September 2009), 1051-1061; Winston Ewert, William A. Dembski, and Robert J. Marks II, “Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism,” Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics (October 2009); Dembski and Marks, “Bernoulli’s Principle of Insufficient Reason and Conservation of Information in Computer Search”; Winston Ewert, George Montanez, William Dembski and Robert J. Marks II, “Efficient Per Query Information Extraction from a Hamming Oracle,” 42nd South Eastern Symposium on System Theory (March 2010), 290-297; Douglas D. Axe, Brendan W. Dixon, and Philip Lu, “Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints,” Plos One 3 (June 2008), e2246.
Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research”; William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Living Systems (Dallas, TX: Foundation for Thought and Ethics, 2008).
Meyer, “The origin of biological information and the higher taxonomic categories”; Kirk K. Durston, David K.Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling 4 (2007), 47; David K.Y. Chiu and Thomas W.H. Lui, “Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis,” International Journal of Fuzzy Systems4 (September 2002), 766-775.
Minnich and Meyer. “Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria”; McIntosh, “Information and Entropy—Top-Down or Bottom-Up Development in Living Systems?”
Jonathan Wells, “Do Centrioles Generate a Polar Ejection Force?,” Rivista di Biologia / Biology Forum, 98 (2005), 71-96; Scott A. Minnich and Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” Proceedings of the Second International Conference on Design & Nature Rhodes Greece (2004); Behe, Darwin’s Black Box; Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity.”
Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity”; Nelson and Jonathan Wells, “Homology in Biology”; Ewert, “The Dependency Graph of Life”; John A. Davison, “A Prescribed Evolutionary Hypothesis,” Rivista di Biologia/Biology Forum 98 (2005), 155-166; Ewert, “The Dependency Graph of Life.”
Sherman, “Universal Genome in the Origin of Metazoa: Thoughts About Evolution”; Albert D.G. de Roos, “Origins of introns based on the definition of exon modules and their conserved interfaces,” Bioinformatics 21 (2005), 2-9; Albert D.G. de Roos, “Conserved intron positions in ancient protein modules,” Biology Direct 2 (2007), 7; Albert D.G. de Roos, “The Origin of the Eukaryotic Cell Based on Conservation of Existing Interfaces,” Artificial Life 12 (2006), 513-523.
Meyer et al., “The Cambrian Explosion: Biology’s Big Bang”; Meyer, “The Cambrian Information Explosion”; Meyer, “The origin of biological information and the higher taxonomic categories”; Lönnig, “Dynamic genomes, morphological stasis, and the origin of irreducible complexity.”
Richard v. Sternberg, “DNA Codes and Information: Formal Structures and Relational Causes,” Acta Biotheoretica 56 (September 2008), 205-232; Voie, “Biological function and the genetic code are interdependent”; David L. Abel and Jack T. Trevors, “Self-organization vs. self-ordering events in life-origin models,” Physics of Life Reviews 3 (2006), 211-228.
Richard v. Sternberg, “On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System”; Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research”; Josiah D. Seaman and John C. Sanford, “Skittle: A 2-Dimensional Genome Visualization Tool,” BMC Informatics 10 (2009), 451.

Our home world: The best seat in the house?

Guillermo Gonzalez on What’s Changed Since The Privileged Planet

Evolution News @DiscoveryCSC

On a classic episode of ID the Future, host Jay Richards and astronomer Guillermo Gonzalez, authors of The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery, discuss what’s changed in the years since the book first appeared. Download the podcast or listen to it here.

One big change they note: the number of exo-planets discovered has exploded, from 200 or so to several thousand. Gonzalez walks through this and other exciting recent advances in astronomy, and the two reflect on how these new discoveries bear upon the predictions and arguments they advanced in their book. Also in the conversation, Gonzalez speculates about what the James Webb Space Telescope may uncover after it comes online.

Primeval tech v. Darwinism:The big picture.

Devo vs. evo?

Cell Fate: Another Hurdle for Evolution

David Coppedge

When a stem cell divides, one daughter cell must maintain its stemness (i.e., ability to differentiate into any cell type) while the other specializes. Therein lies another truckload of requirements for coordinated action that, if it goes awry, can spell disaster for an animal or human. Watch this subject grow into a huge problem for evolutionary theory.

Researchers at University of California at Riverside investigated what happens when stem cells divide and specialize. UCR’s reporter Iqbal Pittawala describes how “genome organization influences cell fate.”

Understanding the molecular mechanisms that specify and maintain the identities of more than 200 cell types of the human body is arguably one of the most fundamental problems in molecular and cellular biology, with critical implications for the treatment of human diseases. Central to the cell fate decision process are stem cells residing within each tissue of the body. [Emphasis added.]

The two daughter cells face a massive organization problem. Even though they contain the same DNA code, they will take on separate roles in the cell. This means that the accessibility of genes between the two cells must radically differ.

Chromatin — a package of DNA wrapped around histone proteins — makes some genes accessible for transcription but hides others from the transcription factors (additional proteins) that switch on transcription. Begin to get a sense of how difficult this will be. There are tens of thousands of genes, and 200 cell types that utilize specific genes but not others. What process determines how chromatin will package the specialist daughter cell to make genes available if it will be a nerve cell as opposed to a muscle cell or heart cell? And how does the system keep the other daughter cell unaltered from the original stem cell?

A Challenge for a Librarian

Biochemist Sihem Cheloufi at UCR, together with colleague Jernej Murn, researched a protein complex involved in the process named “chromatin assembly factor 1” or CAF-1. As you read their description, think of the challenge a librarian faces with the card catalog for a large library.

“To help CAF-1 secure correct chromatin organization during cell division, a host of transcription factors are attracted to open regions in a DNA sequence-specific manner to serve as bookmarks and recruit transcription machinery to correct lineage-specific genes, ensuring their expression,” she said. “We wondered about the extent to which CAF-1 is required to maintain cell-specific chromatin organization during cell division.”

CAF-1 normally keeps genes tightly bound in chromatin so that they are inaccessible to transcription factors.

For a specific case, the biochemists looked at how blood stem cells divide and specialize into neutrophils — a type of white blood cell that acts as a first responder against an invasion by pathogens. They noticed that the levels of CAF-1 are finely balanced to prevent access by a particular transcription factor for that lineage named ELF1. (Note in passing that each cell type has its own suite of lineage-specific transcription factors.) Neutrophils artificially deprived of CAF-1 went awry and forgot their identity.

“By looking at chromatin organization, we found a whole slew of genomic sites that are aberrantly open and attract ELF1 as a result of CAF-1 loss,” Murn said. “Our study further points to a key role of ELF1 in defining the fate of several blood cell lineages.”

Peeking into a Keyhole

Recalling the 200 cell types in the human body, how does CAF-1 organize chromatin for each type? How does it know what genes to make accessible for a kidney cell, an astrocyte in the brain, or a liver cell? The UCR work is peeking into a keyhole of a library with a big operation inside. They don’t yet know how CAF-1 “preserves the chromatin state at specific sites and whether this process works differently across different cell types.” Think of our librarian just starting to get a handle on the job of arranging books in one wing and then finding 200 more wings to manage. Maybe a different analogy will expose the magnitude of this challenge.

“Like a city, the genome has its landscape with specific landmarks,” Cheloufi said. “It would be interesting to know how precisely CAF-1 and other molecules sustain the genome’s ‘skyline.’ Solving this problem could also help us understand how the fate of cells could be manipulated in a predictive manner. Given the fundamental role of CAF-1 in packaging the genome during DNA replication, we expect it to act as a general gatekeeper of cellular identity. This would in principle apply to all dividing cells across numerous tissues, such as cells of the intestine, skin, bone marrow, and even the brain.”

Surely there is much, much more involved than one protein complex named CAF-1. Something needs to “know” how to keep one daughter cell’s chromatin unchanged to maintain the stem cell pool, while reorganizing the chromatin for the differentiating cell — assuming the system also “knows” what cell type that daughter cell must become out of 200 possibilities. This implies a complex signaling system for triggering the production of specific cell types, which must trigger the appropriate suite of protein complexes to package the chromatin for access by that cell type’s lineage-specific transcription factors. Differentiation proceeds down a stepwise transition through progenitor cell states until the specialized cell, such as a neutrophil, results. How many evolutionists have thought about this challenge?

Quality-Control Terms from Engineering

The research paper is published open access. It is Franklin et al., “Regulation of chromatin accessibility by the histone chaperone CAF-1 sustains lineage fidelity,” in Nature Communications. Perhaps the magnitude of the challenge caused the 21 authors to shy away from referring to evolution in the paper. Instead, they refer to “lineage integrity” or “lineage fidelity” a dozen times. Those are quality-control terms from engineering and systems design.

Cell fate commitment is driven by dynamic changes in chromatin architecture and activity of lineage-specific transcription factors (TFs). The chromatin assembly factor-1 (CAF-1) is a histone chaperone that regulates chromatin architecture by facilitating nucleosome assembly during DNA replication. Accumulating evidence supports a substantial role of CAF-1 in cell fate maintenance, but the mechanisms by which CAF-1 restricts lineage choice remain poorly understood. Here, we investigate how CAF-1 influences chromatin dynamics and TF activity during lineage differentiation. We show that CAF-1 suppression triggers rapid differentiation of myeloid stem and progenitor cells into a mixed lineage state. We find that CAF-1 sustains lineage fidelity by controlling chromatin accessibility at specific loci, and limiting the binding of ELF1 TF at newly-accessible diverging regulatory elements. Together, our findings decipher key traits of chromatin accessibility that sustain lineage integrity and point to a powerful strategy for dissecting transcriptional circuits central to cell fate commitment.

Expecting random mutations to somehow emerge then be “selected” by some blind, aimless, uncaring “agentless act” (as Neil Thomas has put it) to construct this complex system seems beyond rational consideration. Intelligent design scientists, though, could make testable predictions to guide further research. Knowing how comparable systems are made by intelligent engineers — that is, systems involving coordinated reorganization of information for multiple applications — they could expect to find new types of sensors, feedback circuits, quality-control checkpoints, or other functional modules at work. These might consist of proteins, protein complexes, small RNAs, sugars, ions, or combinations of them capable of storing or conveying information. (Note: even if automated, these are not “agentless acts.” The agency is one step removed from mind to program, but a mind with foresight was necessary for its origin.)

For example, an ID research team might look for a comparable system in industry that faces the same kind of challenge. They could identify the minimum number of job descriptions required to make the system work, then look for molecules performing those roles in the cellular analogue. Even if the match is imperfect, the ID approach can advance science, because what the researchers learn can feed back into biomimetic design, leading to improved applications in industry.

Poor Darwin. With his crude awareness of cells dividing that looked like bubbles separating, he had no idea what he would be in for in the 21st century.

Wednesday 4 May 2022

The second horseman continues his ride through the slavic world.

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