JEHOVAH'S folly trumps man's wisdom ?

 New Paper on the Panda’s Thumb: “Striking Imperfection or Masterpiece of Engineering?”

Wolf-Ekkehard Lonnig

Readers are invited to consider my new paper,   “The Panda’s Thumb: Striking Imperfection or Masterpiece of Engineering?”The abstract is below.

Abstract: Key Points of the Contents 

Before going further, a brief note on the synonyms that I’m using here such as the “double/dual/complementary function” of the panda’s thumb. Each of the synonyms has its own subtly different overtones. With this in mind, I hope the basic points discussed below may be better understood. 

Above: “Some Key Points in a Long-Lasting Controversy”: Different views of evolutionary biologists on the panda’s thumb. Some assessments of the panda’s dexterity by intelligent design theorists.

Introduction: The panda’s thumb has become a paradigm for evolution in general. Links to articles by Stephen Dilley, and notes on the recent controversy between Nathan Lents and Stuart Burgess.

If the panda’s thumb is an embodiment of bad design, where are the evolutionists’ proposals indicating how they could have done better?

Some citations from a public talk by Stuart Burgess on the ingenious design of the wrist.

A massive contradiction within the theory of evolution itself.

Double/dual/complementary function is often overlooked.

“What makes the modern human thumb myology special within the primate clade is … [the appearance of] two extrinsic muscles, extensor pollicis brevis and flexor pollicis longus.”

It is a fundamental mistake to use the human thumb as a yardstick for the perfection or imperfection of the panda’s thumb.

A closer look at the differences of the radial sesamoid in a basal ursoid in comparison to that of the panda (Ailuropoda) for gripping and walking and the grasping hand of Homo sapiens according to Xiaoming Wang et al. (2022).

In comparison to other bear species, “only in A. melanoleuca can it be considered to be hyper-developed, reaching a similar size to that of the first metacarpal.”

Doubts concerning a simple homology of different sesamoid bones in various species.

Radial sesamoid as the ideal starting point to develop a thumb-like digit in pandas.

Natural selection of the radial sesamoid according to Wang et al. as well as Barrette in contrast to Stanley.

Implications of the ruling neo-Darwinian paradigm (gradualism plus natural selection) for the origin of the panda’s thumb.

Further discussion of Barrette’s points as “the length of the radial sesamoid, and therefore that of the false thumb, is limited firstly by its location under the hand,” etc.

Less efficient feeding would emphasize the enormous problem involved in the theory of natural selection.

The panda’s ecological impact and the “Optimal Panda Principle” in contrast to the evolutionary “Panda Principle” of Gould and his followers.

How to pick up little Necco candy wafers with thumbless mittens?

When directly observing pandas in zoos, Gould and Davis marveled at the dexterity/competence/virtuosity of the panda’s hand. I have done so, too. The panda’s hand is not “clumsy” at all.

Key question from two PhD students at the Max Planck Institute of Plant Breeding Research (Cologne) who came to my office and asked: Wouldn’t it be much more economical for an intelligent designer to modify, as far as possible, an already existing structure for some new functions than to create a totally new structure for similar roles/purposes/tasks from scratch?

Some comments on Barette’s statement that “We owe this metaphor [of approximate tinkering/bricolage] to François Jacob, a French biologist and recipient of the Nobel Prize. Far from being perfect, such approximate tinkering is a trace left by evolutionary history,” and thus a proof of it.

Davis on the enlarged radial sesamoid as “unquestionably” a direct product of natural selection.

Possible number of genes involved in the origin of pandas according to Davis and some others.

What do we know in the interim about panda genetics?

SNPs in the Ursidae including our beloved pandas.

As already mentioned in other articles of mine (for example: https://www.weloennig.de/Hippo.pdf): Note please that virtually all highlighting/emphasis is by W.-E. L. (except italics for genera and species as well as adding a note when the cited authors themselves have emphasized certain points). Why so often? Well, since many people do not have the time to study a more extensive work in detail, these highlights can serve as keywords to get a first impression of what is being discussed. 

Concerning the key points enumerated above: Page numbers may change in a future update, and so are not presented here. Incidentally, citations do not imply the agreement of the authors quoted with my overall views nor vice versa. Moreover, I alone am responsible for any mistakes.

On questions concerning absolute dating methods, see http://www.weloennig.de/HumanEvolution.pdf, p. 28. 

technology of the zygote vs. Darwin.

 Let’s Think About a Zygote Like an Engineer

Howard Glicksman

Having read Evolution News for years, contributing an occasional article or two, in addition to my 81-part series on “The Designed Body,” I’ve noticed that there’s a certain way we proponents of intelligent design tend to frame our arguments. We usually provide information on what it takes for life to work, rather than just how it looks (per much of neo-Darwinism). Then we look for reasonable explanations of causation which must include where the information came from to properly produce, assemble, and coordinate all the necessary parts of a given system that we know is absolutely needed for survival (most of that is absent from neo-Darwinism).

But in my collaboration with Steve Laufmann to produce our book Your Designed Body, we came to the conclusion that a different style may be more useful. What we propose is that, in addition to what’s described above, we also engage readers with examples of “problem-solving” just like engineers do it. After all, it takes one to know one. If you’ve never used mental energy to try to solve any one of these hard problems of life, then how can you appreciate what it took to come up with and apply the solution? 

Let’s try the following as an exercise. Once you’ve gone through it, you’ll be better prepared to understand all the causal hurdles that had to have been surmounted. And this will allow you to ask better questions and not be as vulnerable to many of the “just so” stories of neo-Darwinism. 

“Separation of Concerns”

Recently, there was an article in The Scientist, “The First Two Cells in a Human Embryo Contribute Disproportionately to Fetal Development.” It noted a study published in Cell, “The first two blastomeres contribute unequally to the human embryo,” indicating that “a research team showed that, contrary to current models, one early embryonic cell dominates lineages that will become the fetus.” 

The gist of the article was that the current thinking — that it’s at the eight-cell stage where totipotent embryonic cells take the first “fork in the road” of commitment to developing into the fetus or the placenta — may be incorrect. It would now seem that this first “separation of concerns” (as Laufmann and I call it) may take place earlier on, when the zygote divides into the first two blastomeres. 

Ingenious methods were used to label and track the cell lineage from the two-cell to the blastocyst stage:“Thus, they could determine the contribution of each cell to the development of two early structures: the trophectoderm (TE) that becomes the placenta and the inner cell mass (ICM) that eventually produces the fetal tissue.” 

“They are not identical,” explains Magdalena Zernicka-Goetz, a developmental and stem cell biologist at Caltech and the University of Cambridge who is a study co-author. “Only one of the two cells is truly totipotent, meaning it can give rise to body and placenta, and the second cell gives rise mainly to placenta.” She adds, “I was always interested in how cells decide their fate.” The article in The Scientist concludes by telling us that “next, Zernicka-Goetz aims to investigate the features and origins of the differences between clones at the two-cell stage.”

Points to Ponder

It is clear that scientists still do not fully understand how human life develops from the zygote to a newborn and then into a mature fertile adult. One has to wonder what signaling and communication must take place at exactly the right times and in the right orders for all of this to happen properly, never mind where the information and instructions came from. Despite this self-acknowledged lack of understanding, we are told by evolutionary science that it certainly was an unguided and undirected natural process that brought it into being, and not a mind at work, as intelligent design contends. 

What do you think? If you took your car to a mechanic and he told you that he has no idea what’s wrong with it but he’s sure he can fix it, would you engage his services? Just because the scientist is smarter than you about what parts do what and how, that doesn’t necessarily mean that her conclusions about causation are true. After all, in saying that “I was always interested in how cells decide their fate,” she’s attributing agency, a mind at work, to the zygote. So don’t be misled.

Human Life Is a Hard Problem

Actually, life is a series of millions of hard problems that have to be solved all the time, or else. I’m talking about, among many other things, the cellular, metabolic, anatomical, and neuromuscular problems of human life. Let’s start from square one — the human zygote — how each of us began after the sperm of our father joined with the egg of our mother within her womb. That is the one cell from which, within nine months, we developed into a three-trillion-cell newborn with all the equipment we needed to survive. 

If you could go back in time to that moment in your life, be nanosized and micro-pipetted into your own first cell, what would be the first problem you’d have to solve? In other words, once the zygote comes into being, what’s the first thing it has to do? 

Well, if it’s going to become a newborn in nine months or so, it’s got to start dividing. But that won’t happen for at least 24 hours, so you have to consider what else may be more important as the zygote floats within the fluid of your mom’s uterus.

The chemical content of the fluid inside the zygote (high potassium, low sodium) is the opposite of what’s in the fluid surrounding it (low potassium, high sodium). And because these ions can cross the cell membrane, diffusion would naturally make them try to equalize on both sides (inside and outside the zygote) which would spell disaster. So, the sodium/potassium pumps in the zygote’s cell membrane have to kick in right away to keep pushing sodium out and bringing potassium back in, right?

Yes, the action of the million or so sodium/potassium pumps in the zygote’s cell membrane are needed for it to stay alive. But what do they need to do their work?

All work requires energy. So, as with all of life, the first priority of the zygote is to generate enough energy through glycolysis (without oxygen) and cellular respiration (with oxygen). The zygote needs oxygen and glucose (or other substances) to metabolize to get the energy it needs.

And if the zygote’s going to divide into two cells, then four, eight, sixteen, and more, then it’s also going to need nutrients to be able to make more copies of itself. Where does the new human life get the oxygen and nutrients it needs, and how does it make sure of its supply until it becomes a newborn? 

The Engineering Problem

This is how Steve Laufmann and I framed this engineering problem in our book:

All cells need oxygen and nutrients. Early life is no exception. Fertilization results in a zygote, which multiplies through cell division to become an embryo. In the early phase, the embryo gets what is needed by diffusion from the surrounding fluid. This works when there’s only a few dozen cells. But within several weeks the embryo will grow into a fetus, and in a few months into a newborn with trillions of specialized cells organized into coherent, interdependent, finely tuned organ systems. For this to be possible, the embryo needs a better way to get oxygen and nutrients, and to get rid of carbon dioxide and waste materials. If he cannot meet this challenge, he will not survive. But he’s in a special situation, dwelling inside his mother, so he’ll need a solution altogether different from anything else in the body’s inventory — a distinct yet temporary system that can meet this need while he’s developing his permanent internal systems.

We go on to ask a very important engineering question:

How do you build a series of finely tuned, coherent interdependent systems, each necessary for life, and stay alive the whole time? It just wouldn’t do if the body needed to go dead for a while, build some stuff, then come back to life when everything was ready to go. What the child in the womb needs is a complete set of temporary systems to meet the needs of his rapidly growing body, to keep it alive until its own systems are ready to take over. Then at birth, when they are no longer needed, these systems must be discarded as the child transitions to long-term systems.

The Solution Is the Placenta

The  answer to the very hard engineering problem we asked above is the placenta. Somehow or other the zygote has the foresight to know that down the road it will develop into a fetus that requires the placenta for its metabolic and nutritional needs. 

This is how we explain the solution in our book:

           Tissues of the embryo (TE) combine with tissues of the mother (lining of the uterus) to make the placenta — a totally separate organ that provides the scaffolding needed to keep the developing child alive. The placenta enables the mother to sustain the developing child while his internal organ systems and tissues are being fabricated, integrated, and launched. The developing child is, quite literally, on life support between the zygote phase and birth, when his body is finally ready to take over the job.

Up until this recent study it was thought that it’s not until the embryo consists of at least eight cells that some of them start to commit to being part of the placenta (TE). But now it seems that it takes place at the two-cell stage. If your nanosized self is inside the zygote, which lever do you pull to make sure that one of the two forming blastomeres goes down the TE-track? And even more important, where did the lever come from? 

It appears that, based on the findings of this study, the answer to the first question will be the concern of future research. But since, as we are regularly assured, we all know that life came about from the unguided and undirected processes of natural selection acting on random variation, the second question is assumed to have already been answered back in 1859, before we knew any of these intricate particulars and when biological systems were assumed to be vastly simpler than they turned out to be. What do you think? Any questions?

More light ,less heat re:dark matter?

 

The plague of plagues?

 

Predarwinian design vs. Darwinism

 Life Can’t Exist Without Repair Mechanisms, and That’s a Problem for Origin-of-Life Theories

Rob Stadler

A cell is often described as a factory — a quite extraordinary factory that can run autonomously and reproduce itself. The first cell required a lengthy list of components, layers of organization, and a large quantity of complex specified information, as described by previous episodes of Long Story Short. The latest entry in the series emphasizes yet another requirement for life: an abundance of specific repair mechanisms. 

Damage to the “factory” of the cell occurs on two levels: damage to the stored information (either during replication or by natural degradation over time) and damage to the manufacturing machinery (either from faulty production of new machinery or damage incurred during use). Each type of damage requires specific repair mechanisms that demonstrate foresight — the expectation that damage will occur and the ability to recognize, repair and/or recycle only those components that are damaged. All known life requires these mechanisms. 

Damage to Stored Information

The initial process of DNA replication is facilitated by a polymerase enzyme which results in approximately one error for every 10,000 to 100,000 added nucleotides.1 However, no known life can persist with such a high rate of error, if left uncorrected.2 Fortunately, DNA replication in all life includes a subsequent proofreading step — a type of damage repair — that enhances the accuracy by a factor of 100 to 1,000. The current record holder for the sloppiest DNA replication of a living organism, under normal conditions, is Mycoplasma mycoides (and its human-modified relative, JVCI-syn 3A), where only 1 in 33,000,000 nucleotides are incorrectly copied.3

Following the replication of DNA, a daily barrage of DNA damage occurs during normal operating conditions. Life therefore requires sophisticated and highly specific DNA repair mechanisms. In humans, DNA damage response is estimated to involve a hierarchical organization of 605 proteins in 109 assemblies.4 Efforts to make the simplest possible cell by stripping out all non-essential genes has successfully reduced DNA repair to a minimal set of six genes.5 But, these six genes are encoded in thousands of base pairs of DNA, and the machinery to transcribe and translate those genes into the repair enzymes requires a minimum of 149 genes.6 Thus, the DNA code that is required to make DNA repair mechanisms easily exceeds 100,000 base pairs. Here, we encounter a great paradox, first identified in 1971 by Manfred Eigen7: DNA repair is essential to maintain DNA but the genes that code for DNA repair could not have evolved unless the repair mechanisms were already present to protect the DNA. 

Faulty Production of New Machinery

We  used to think that the metabolic machinery in a cell always produced perfect products. But the reality is that faulty products are unavoidable, resulting in the production of interfering or toxic garbage. All living organisms must therefore have machinery that identifies problems and either repairs or recycles the faulty products. 

The cell’s central manufacturing machine is the ribosome, a marvel that produces functional proteins from strands of mRNA (with the help of many supporting molecules). Unfortunately, about 2-4 percent of mRNA strands get stuck in the ribosome during translation into a protein.8 Not only does this halt production, but it could result in production of a toxic, half-finished protein. 

If the mitochondria could not get “unstuck,” life as we know it would end. In the process of self-replication, a single cell must produce an entire library of proteins, placing a heavy burden on the cell’s mitochondria. But with a 2-4 percent rate of stuck mRNA strands, the average cell would have each of its mitochondria get stuck at least five times before the cell could replicate.9 Therefore, life could never replicate and metabolism would cease unless this problem was solved.

Fortunately, all forms of life, even the simplest,9 are capable of trans–translation, typically involving a three-step process. First, a molecule combining transfer and messenger RNA and two helper molecules (SymB and EF-Tu) recognizes that mRNA is stuck in the ribosome and attaches a label to the half-formed protein. This label, called a degron, is essentially a polyalanine peptide. The condemned protein is recognized, degraded, and recycled by one of many proteases. Finally, the mRNA must also be labeled and recycled to keep it from clogging other ribosomes. In some bacteria,10 a pyrophosphohydrolase enzyme modifies the end of the mRNA, labeling it for destruction. An RNAse (another enzyme) then recognizes this label, grabs hold of the mRNA, and draws it close to its magnesium ion, which causes cleavage of the RNA. Another RNAse then finishes the job, breaking the mRNA up into single nucleotides which can be re-used.

The required presence of tools that can destroy proteins and RNA also comes with a requirement that those tools are highly selective. If these tools evolved, one would expect the initial versions to be non-selective, destroying any proteins or RNA within reach, extinguishing life and blocking the process of evolution.11

Note that the set of tools for trans-translation and protein and RNA recycling are all stored in DNA, which must be protected by repair mechanisms. And, these tools cannot be produced without mitochondria, but the mitochondria cannot be unstuck without the action of trans-translation. Thus, we encounter another case of circular causality. 

Damage Incurred During Use

The normal operation of enzymes or metabolites like co-enzymes or cofactors involves chemical reactions that follow specific paths. Deviations from the desired paths can occur from interferences like radiation, oxidative stress, or encountering the wrong “promiscuous” enzyme. These deviations result in rogue molecules that interfere with metabolism or are toxic to the cell. As a result, even the simplest forms of life require several metabolic repair mechanisms: 

“[T]here can be little room left to doubt that metabolite damage and the systems that counter it are mainstream metabolic processes that cannot be separated from life itself.”12

“It is increasingly evident that metabolites suffer various kinds of damage, that such damage happens in all organisms and that cells have dedicated systems for damage repair and containment.”13

As a relatively simple example of a required repair mechanism, even the simplest known cell (JVCI Syn 3A) has to deal with a sticky situation involving sulfur. Several metabolic reactions require molecules with a thiol group — sulfur bonded to hydrogen and to an organic molecule. The organism needs to maintain its thiol groups, but they have an annoying tendency to cross link (i.e., two thiol groups create a disulfide bond, fusing the two molecules together). Constant maintenance is required to break up this undesired linking. Even the simplest known cell requires two proteins (TrxB/JCVISYN3A_0819 and TrxA/JCVISYN3A_0065) to restore thiol groups and maintain metabolism.12 Because the repair proteins are themselves a product of the cell’s metabolism, this creates another path of circular causality: You can’t have prolonged metabolism without the repair mechanisms but you can’t make the repair mechanisms without metabolism.

An Ounce of Prevention is Worth a Pound of Cure

In addition to life’s required repair mechanisms, all forms of life include damage prevention mechanisms. These mechanisms can destroy rogue molecules, stabilize molecules that are prone to going rogue, or guide chemical reactions toward less harmful outcomes. As an example, when DNA is replicated, available monomers of the four canonical nucleotides (G, C, T, and A) are incorporated into the new strand. Some of the cell’s normal metabolites, like dUTP (deoxyuridine triphosphate), are similar to a canonical nucleotide and can be erroneously incorporated into DNA. Even the simplest cell (once again, JVCI-syn3A) includes an enzyme (deoxyuridine triphosphate pyrophosphatase) to hydrolyze dUTP and prevent formation of corrupted DNA.6

Summing Up the Evidence

Those who promote unguided abiogenesis simply brush off all of these required mechanisms, claiming that life started as simplified “proto-cells” that didn’t need repair. But there is no evidence that any form of life could persist or replicate without these repair mechanisms. And the presence of the repair mechanisms invokes several examples of circular causality — quite a conundrum for unintelligent, natural processes alone. Belief that simpler “proto-cells” didn’t require repair mechanisms requires blind faith, set against the prevailing scientific evidence.   

Notes

Babenek A, and Zuizia-Graczyk I. Fidelity of DNA replication — a matter of proofreading. Curr Genet. 2018; 54: 985-996.

Some viruses have high error rates when replicating, but viruses cannot replicate without the help of cellular life, which requires very low error rates. Some specialized DNA polymerases intentionally operate with lower fidelity on a temporary basis for purposes such as antibody diversity. 

Moger-Reischer RZ, et al. Evolution of a Minimal Cell. Nature. 2023; 620: 122-127.

Kratz A, et al. A multi-scale map of protein assemblies in the DNA damage response. Cell Systems 2023; 14: 447-463.

Hutchison CA, et al. Design and synthesis of a minimal bacterial genome. Science 2016; 351: aad6253. 

Breuer M, et al. Essential Metabolism for a Minimal Cell. eLife 2019;8:e36842 DOI: 10.7554/eLife.36842. 

Eigen, M. Self-organization of matter and evolution of biological macromolecules. Naturwissenschaften, 1971; 58: 465–523.

Ito K, et al. Nascentome analysis uncovers futile protein synthesis in Escherichia coli. PLoS One 2011; 6: e28413

Keiler KC, Feaga HA. Resolving nonstop translation complexes is a matter of life or death. Journal of Bacteriology 2014; 196: 2123-2130.

Mackie GA. RNase E: at the interface of bacterial RNA processing and decay. Nature Reviews Microbiology 2013; 11: 45-57.

“Because RNA degradation is ubiquitous in all cells, it is clear that it must be carefully controlled to accurately recognize target RNAs.” Houseley J and Tollervey D. The many pathways of RNA degradation. Cell 2009; 136: 763-776.

Hass D, et al. Metabolite damage and damage control in a minimal genome. American Society for Microbiology 2022; 13: 1-16.

Linster CL, et al. Metabolite damage and its repair or pre-emption. Nature Chemical Biology 2013; 9: 72-80.

Designed evolution vs. evolved design?.

 

Common design vs. Common descent.

 New Paper Argues that Variant Genetic Codes Are Best Explained by Common Design

Jonathan McLatchie

A popular argument for a universal common ancestor is the near-universality of the conventional genetic code. Critics of common descent often point to deviations from the standard code as evidence against it. A recent paper published in the journal BIO-Complexity, by Winston Ewert, reviews the character and distribution of genetic code variants and the implications these have for common ancestry, and “develops a framework for understanding codes within a common design framework, based crucially on the premise that some genetic code variants are designed and others are the result of mutations to translation machinery.” Ewert explains that,

Upon first investigation, evolutionary theory appears to have a compelling account of the character and distribution of variant codes. Evolutionary theory suggests that if genetic code evolution is possible it should be very rare. This would explain why most genomes follow the standard code and why the exceptions only vary in a few codons. It would also explain the following details about the variant codes. Most variations are found in mitochondria, whose very small genomes would make code evolution easier. Many variations are also found in highly reduced genomes, such as those of endosymbiotic bacteria. No variations are found in the nuclear genomes of complex multicellular organisms like plants and animals. The distribution of many codes can be easily explained by identifying certain points on the tree of life where codons were reassigned and then inherited by all of their descendants.

EWERT W (2024) ON THE ORIGIN OF THE CODES: THE CHARACTER AND DISTRIBUTION OF VARIANT GENETIC CODES IS BETTER EXPLAINED BY COMMON DESIGN THAN EVOLUTIONARY THEORY. BIO-COMPLEXITY 2024 (1):1-25.

Three Tenets

The paper proposes “a framework that seeks to explain the character and distribution of variant genetic codes within a common design framework.” Ewert’s framework has three tenets: First, “the canonical genetic code has been well optimized and is thus an ideal choice for most genomes.” There are multiple optimized parameters and thus “A designer must identify the best trade-offs to select the ideal genetic code.” The second tenet of Ewert’s framework is that a minor variation on the standard code is better suited to some organisms, since those organisms may acquire an advantage by a different set of trade-offs with respect to genetic code optimization. The third tenet is that the translation machinery has been damaged by mutations in some organisms, and that this has resulted in their misinterpreting the code they were initially designed to employ. These are examples of genetic code variants that have evolved naturally.

Five Criteria

Ewert offers five criteria that may be used to distinguish genetic codes that are evolved from those that are designed. First, evolved codes are expected to be found in taxonomic groups below the family level, whereas those that are designed are predicted to be above the level of family. Second, evolved codes should be readily “explicable in terms of some simple mutation to the translation machinery of the cell.” Third, it is predicted that codes that are evolved will be limited to the genomes of endosymbionts. Fourth, it is expected that codes that are evolved utilize a small number of codons so that the variation does not cause the organism too much harm. Fifth, it is predicted that evolved codes will fall into a simple nested hierarchical (phylogenetic) distribution. By contrast, 

[D]esigned codons are found in high-level taxa of at least genus-level but typically higher. They involve many reassignments that are difficult to explain with any sort of simple mutation. They are found in free-living organisms. They sometimes reassign codons that are expected to be rare. They are often distributed in a complex fashion that does not fit phylogenetic expectations.

EWERT W (2024) ON THE ORIGIN OF THE CODES: THE CHARACTER AND DISTRIBUTION OF VARIANT GENETIC CODES IS BETTER EXPLAINED BY COMMON DESIGN THAN EVOLUTIONARY THEORY. BIO-COMPLEXITY 2024 (1):1-25.

It has been conventionally thought that evolution provides a good explanation for the character and distribution of genetic code variants — in particular, the near-universality of the standard code; the prevalence of variant codes in simple genomes such as those of mitochondria; and the phylogenetic distribution of variant codes. Ewert notes that, in light of evolutionary theory, it would in fact be expected that there would be variant codes found at the higher taxonomic levels, which would be consistent with the genetic code still being variable at the time of the last common ancestor. However, “What we observe instead are modifications of the standard code. They are not associated with the high-level taxa…” 

Furthermore, though we should expect on evolutionary theory that it would be exponentially harder to reassign a code as the number of genes increases, “variant codes are found in nuclear genomes that are not particularly small. They are found in ciliates, which have comparable numbers of genes to the human genome. Additionally, we find them in some multicellular green algae. In fact, we find more code variation in eukaryotic nuclear genomes than in bacterial genomes, despite eukaryotes having much larger genomes.” Thus, Ewert concludes, “despite the initial impression, evolutionary theory does not account well for the kinds of genomes with variant codes.”

Invoking “Inexplicable Events”

Finally, though evolutionary theory would predict that the distribution of variant codes would be consistent with the standard phylogeny, Ewert observes that, “In many cases, the distribution of a code is complex, defying evolutionary explanations. Codes recur in closely related groups in a way not explained by common descent. Evolutionary theory has to invoke inexplicable events such as reversions to the standard code.”

Thus, Ewert concludes, “Initially, evolutionary theory appeared to have some explanatory power. However, upon closer inspection, the features of the variant codes that seemed well explained by evolutionary theory turned out to either be inaccurate or to not follow from evolutionary theory.” Instead, he argues that the character and distribution of variant codes is often better explained under a framework of common design.

The paper is well worth a careful read. It can be accessed here.

Yet another house divided?

 

The future we were promised is finally here?

 

Making the case for actual design in nature.

 

Toward the edge of Darwinism.

 

Every silver lining has a cloud?

 

Settled science is the real science stopper?

 

Thoughtful Darwinism to ID : lets be frenemies II

 Evolutionary Biologist Concedes Intelligent Design Is the Cutting Edge

David Klinghoffer

Bret Weinstein and Heather Heying are well-known evolutionary biologists (and husband and wife) with a podcast, the DarkHorse Podcast. Recently Weinstein posed a provocative question, “Is intelligent design a competitor to Darwinian evolution?” His answer may surprise you: Yes.  

No, he’s not about to come over to the dark side. Weinstein is confident that Darwinism will meet the challenges that ID has set, about the Cambrian Explosion and more, but he concedes that it hasn’t done so yet.

He describes conversations with Richard Dawkins and Jerry Coyne, asking them why evolutionary biology hasn’t had a breakthrough since 1976 when Dawkins published The Selfish Gene. Dawkins and Coyne, separately, both answered that it was because all the big questions had already been answered, and all that was left was a “clean up” operation. Weinstein recognizes that that is just so much blowing smoke, and the work of Stephen Meyer and his “high-quality colleagues” in the ID research community has exposed the problems that Darwinists need to be working on to solve. 

Settled Science?

About Dr. Meyer, he says:

           I encountered people like Stephen Meyer, who were not phony scientists, pretending to do the work. They were actually very good at what they did. And I believe Stephen Meyer is motivated by a religious motivation, but we don’t generally ask the question when somebody takes up science, “What are you really in it for? Are you in it for the fame?” That’s not a legitimate challenge to somebody’s work. 

And the fact is, Stephen Meyer is very good at what he does. He may be motivated by the thought that at the end of the search he’s going to find Jesus. But in terms of the quality of his arguments, I was very impressed when I met him: his love for biology, his love for creatures, the weirder the better, he likes them, right? So that looked very familiar to me. 

No Mind Readers Here

In other words, motivation should be irrelevant. The quality of the science is what counts. I would add, none of us is a mind reader and we can never know what someone else’s motivation really is. In any event, says Weinstein, ID clearly is about science, not religion:

And it all also became obvious to me in interacting with Stephen Meyer and many of his high-quality colleagues that they’re actually motivated, for whatever reason, to do the job that we are supposed to be motivated to do inside of biology. They’re looking for cracks in the theory. Things that we haven’t yet explained. And they’re looking for those things for their own reasons, but the point is we’re supposed to be figuring out what parts of the stories we tell ourselves aren’t true, because that’s how we get smarter over time. 

Shrinking from a Fight 

Darwinists, say Weinstein, are shrinking from a fight they wrongly feel they shouldn’t have to bother with:

If you decide… that your challengers aren’t entitled to a hearing because they’re motivated by the wrong stuff, then you do two things. One, you artificially stunt the growth of your field, and you create a more vibrant realm where your competitors have a better field to play in because you’ve left a lot of holes in the theory ready to be identified, which I think is what’s going on. The better intelligent design folks are finding real questions raised by Darwinism, and the Darwinists, instead of answering those questions, [are] deciding it’s not worthy of their time. And that is it is putting us on a collision course.

“Giving Up Darwin”

Heying cites the 2019 public defection from Darwinism of Yale computer scientist David Gelernter, who pointed to Meyer’s writing as his primary reason for “Giving Up Darwin.” She admits she hasn’t kept up with the challenges from ID, but agrees that she should keep up, and that’s because challenges like those from ID can make the evolutionary establishment “smarter.” Ignoring the challenges makes the establishment dumber — stagnant and self-satisfied.

I’m not familiar with most of the arguments that are coming out of the intelligent design movement. It hasn’t felt like it was my obligation to be familiar with them. Perhaps what you’re arguing is it is our responsibility.

Weinstein, unlike Coyne or Dawkins, is up for talking and debating with ID proponents:

I’m open to that battle and I expect that if we pursue that question, what we’re going to find is, oh, there’s a layer of Darwinism we didn’t get and it’s going to turn out that the intelligent design folks are going to be wrong. But they will have played a very noble and important role in the process of us getting smarter. And look, I think Stephen Meyer at the end of the day, I don’t think he’s going to surrender to the idea that there’s no God at the end of this process. But if we find a layer of Darwinism that hasn’t been spotted, that answers his question, I think he’s going to be delighted with it the same way he’s delighted by the prospect of seeing whale sharks.

Again, these are remarkable concessions from a couple of scientists who are not at all looking to make the leap to ID, but who understand that intelligent design, not Darwinism, is currently at biology’s cutting edge.

Yet more on the fossil records anti Darwinian bias

 Fossil Friday: Ediacaran Animal Embryos Put to Test and Put to Rest

Gunter Bechly

The Weng’an biota of the Doushantuo Formation in South China is a famous fossil Lagerstätte, which is of particular importance, because it is dated to an Early-Middle Ediacaran age (590-575 million years ago), right in the time when molecular clock estimates place the origin of crown group metazoan animal phyla. The absence of actual unequivocal fossil animals from this period has often been explained away as an artifact of an incomplete fossil record. However, the discovery of various Ediacaran localities of the Burgess-Shale-Type decisively refuted this artifact hypothesis (Bechly 2020b), because those localities would have easily preserved any early small and soft-bodied animals, but only yielded macroalgae and a few problematic forms of uncertain affinity.

The Last Straw

The phosphatized microfossils of the Doushantou Formation, which are three-dimensionally preserved down to the cellular level, represent the last straw to somehow align the molecular clock expectations with the actual fossil record. This explains the urge by paleontologists to readily interpret some of the Doushantuo fossils as metazoan embryos. To the great frustration of evolutionists, all these attempts proved to be highly contentious and ultimately failed to provide any convincing evidence for Ediacaran metazoans. I discussed the dubious nature of these alleged animal embryos in several previous articles (Bechly 2020a, 2020b, 2022a; also see Evolution News 2016), where you can also find all the references to the peer-reviewed literature.

Now a new study by Sun et al. (2024), published in the Proceedings of the Royal Society, looks at the developmental biology of the genus Spiralicellula that was previously proposed as a potential metazoan embryonic stage, a kind of planktonic larva. The authors found a very different developmental mode exhibited by Spiralicellula and all the other alleged metazoan embryos, lacking any cell differentiation, compared to any crown group metazoans. They therefore explicitly “reject a crown-metazoan affinity for Spiralicellula and all other components of the Weng’an biota, diminishing the probability of crown-metazoan diversification before the early Ediacaran.” The authors do not even consider Spiralicellula as a plausible stem-animal but conclude “that Spiralicellula is more likely affiliated with non-metazoan holozoans than with stem metazoans.” So the highly critical view that I elaborated in my previous articles is still well in line with the most recent mainstream research by the leading experts on these fossils.

A New Study

Therefore, it is well worth quoting at some length from the conclusions of this interesting and important new study:

While the embryo-like fossils from the Weng’an biota were once thought to represent the earliest metazoans, recent research has suggested that some species, including Caveasphaera [40], Helicoforamina [29], Ostiosphaera [47], Sporosphaera [33] and now Spiralicellula, have affinities that lie outside crown Metazoa. Interpretations of soma–germ cell differentiation in Megasphaera [21] have been used to support their interpretation as stem metazoans, at best. The primary evidence for a stem-metazoan affinity of Megasphaera derives from ‘matryoshka’ structures that are interpreted to reflect cell differentiation. Nevertheless, it remains unclear whether these structures are endogenous or exogenous in origin [7,48]….

The Weng’an biota, renowned for its exceptional preservation fidelity, is considered a distinctive taphonomic window that holds great potential for documenting the earliest metazoans. The absence of definitive evidence of crown metazoans in the biota is inconsistent with the expectations of the molecular clock estimates which posit a Tonian or Cryogenian origin for the clade [1,2]. It remains formally possible that the absence of crown-group animals from the Weng’an biota and earlier strata reflects the incompleteness of the fossil record, and the discovery of unequivocal metazoans from the Weng’an biota or older strata remains a viable possibility, not least given the discovery of crown metazoans, including cnidarians and bilaterians, within the later Ediacaran [50–54]. However, claims of crown metazoans from the Cryogenian [55,56] and Tonian [57,58] are all highly contested [59–62] and intense exploration of the Weng’an biota, the most exceptional of all sites of fossil preservation, has failed to yield the anticipated evidence of early crown metazoans, instead yielding only evidence of non-metazoan holozoans or possible stem metazoans. Alongside the Weng’an biota, the Doushantuo silicified Lagerstätte in South China serves as its lateral counterpart [28,63–65]. Despite differing preservational settings, this Lagerstätte remarkably preserves fossil structures down to a subcellular level. It contains a diverse array of microfossils, including cyanobacteria, acritarchs, multicellular algae, and embryo- like fossils [63,66,67], all found in the Weng’an biota. Notably absent, however, are fossils of crown-group metazoans. As such, the available fossil evidence suggests a relatively low probability of crown metazoans diversifying in the early Ediacaran, rather than ecological constraints within the Weng’an biota’s preservational setting. Such insights prompt a recalibration of molecular timescales in light of these discoveries.

In short: There are no fossil animals in the Ediacaran, when they should be found according to the gradualistic predictions of Darwinian evolution and according to molecular clock datings. The fossil record does not agree with either of these predictions, so that the theory fails the empirical test.

Time for a Better Theory!

In his New York Times bestseller book Darwin’s Doubt, Stephen Meyer (2013) considered that the Ediacaran Doushantuo fossils may indeed include actual animal embryos of sponges. As I have already indicated (Bechly 2020b, 2022a, 2022b), this concession may have been far too generous. Even mainstream evolutionist science more and more recognizes that there simply are no metazoan animal embryos in the Doushantuo Formation. So, where are all the postulated ancestors of the more than twenty different animal phyla appearing abruptly in the Cambrian Explosion? Even Richard Dawkins (2009) has admitted that the Cambrian shows us a substantial number of major animal phyla “already in an advanced state of evolution, the very first time they appear. It is as though they were just planted there, without any evolutionary history. Needless to say, this appearance of sudden planting has delighted creationists.” Well, maybe nature is telling you something.

References

Bechly G 2020a. The Myth of Precambrian Sponges. Evolution News May 12, 2020. https://evolutionnews.org/2020/05/the-myth-of-precambrian-sponges/

Bechly G 2020b. The Demise of the Artifact Hypothesis. Evolution News June 6, 2020. https://evolutionnews.org/2020/07/demise-of-the-artifact-hypothesis-aggravates-the-problem-of-the-cambrian-explosion/

Bechly G 2022a. “Lying on the Internet”? Debunking Dave Farina on Stephen Meyer. Evolution News December 1, 2022. https://evolutionnews.org/2022/12/lying-on-the-internet-debunking-dave-farina-on-stephen-meyer/

Bechly G 2022b. Let’s Help “Professor Dave” Understand the Precambrian. Evolution News December 2, 2022. https://evolutionnews.org/2022/12/lets-help-professor-dave-understand-the-precambrian/

Dawkins R 2009. The Greatest Show on Earth. Free Press, New York (NY), 470 pp.

Evolution News 2016. New Precambrian Embryos Are equivocal at Best. Evolution News August 18, 2016. https://evolutionnews.org/2016/08/new_precambrian_1/

Meyer SC 2013. Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. HarperOne, New York (NY), viii+498 pp.

Sun W, Yin Z, Liu P, Zhu M & Donoghue P 2024. Developmental biology of Spiralicellula and the Ediacaran origin of crown metazoans. Proceedings of the Royal Society B 291: 20240101, 1–10. DOI: https://doi.org/10.1098/rspb.2024.0101

The carbon atom vs. Darwin.

The Remarkable Carbon Atom

Jonathan McLatchie 

In an article yesterday, I discussed the incredible design of the nonmetal atoms, and the striking coincidence that the very atoms from which one can build stable, defined shapes also give us the hydrophobic force, which is the key to arranging them into higher-level structures. Here, I will discuss the fitness of carbon for life, and the incredibly fortuitous circumstances that promote its abundance in the universe.

The Fitness of Carbon for Life

The carbon atom, the primary constituent of organic molecules, is, in several respects, uniquely fit for the assembly of the complex macromolecules found in the cell. First, due to the stability of carbon-carbon bonding, only carbon can form long polymers of itself, forming long chains or rings, while also bonding to other kinds of atoms. Though silicon can also form long chains by bonding with itself, these bonds are significantly less stable than carbon-carbon bonds. Plaxco and Gross note that “while silicon-silicon, silicon-hydrogen, and silicon-nitrogen bonds are similar in energy, the silicon-oxygen bond is far more stable than any of the other three types. As a consequence, silicon readily oxidizes to silicon dioxide, limiting the chemistry available to this atom whenever oxygen is present. And oxygen is the third most common atom in the Universe.”1 As Primo Levi explains, carbon “is the only element that can bind itself in long stable chains without a great expense of energy, and for life on earth (the only one we know so far) precisely long chains are required. Therefore carbon is the key element of living substance.”2

Second, carbon is tetravalent — that is, each atom can form four covalent bonds with other atoms. Third, carbon possesses a relatively small atomic nucleus, entailing short bond distances, thereby allowing it to form stable bonds with itself as well as other atoms. This property is also possessed by the other small, non-metal atoms in period two. Carbon is able to form single, double, and triple bonds with other atoms. Nitrogen can also form single, double, or triple bonds and oxygen can form single and double bonds. Contrast this with the nonmetal atoms directly beneath them in the periodic table — silicon, phosphorus, and sulfur — which possess larger atomic radii and therefore form such bonds less easily due to multiple bonds having reduced stability. 

Another property of organic bonds is that their strength sits within a Goldilocks zone, being neither too strong nor too weak for biochemical manipulations in the cell. If the strength of those bonds were to be altered by a single order of magnitude, it would render impossible numerous biochemical reactions that take place in the cell. If it were too strong, the activation energy needed to break bonds could not be sufficiently reduced by enzymatic activity (enzymes strain chemical bonds by engaging in specific conformational movements while bound to a substrate). Conversely, if organic bonds were much weaker, bonds would be frequently disrupted by molecular collisions, rendering controlled chemistry impossible. 

Another special characteristic of carbon is that there is not much variation in energy levels of carbon bonds from one atom to the next. Robert E. D. Clark explains that carbon “is a friend of all. Its bond energies with hydrogen, chlorine, nitrogen, oxygen, or even another carbon differ little. No other atom is like it.”3 Kevin W. Plaxco and Michael Gross further comment, “Carbon presents a fairly level playing field in which nature can shuffle around carbon-carbon, carbon-nitrogen, and carbon-oxygen single and double bonds without playing too great a cost to convert any one of these into another… Given all this, it’s no wonder that on the order of ten million unique carbon compounds have been described by chemists, which is as many as all of the described non-carbon-containing compounds put together.”4

Carbon Resonance

As we have seen, carbon is absolutely fundamental to life. It also happens to be — after hydrogen, helium, and oxygen — the fourth most abundant element in our galaxy. A carbon nucleus can be generated by smashing together two nuclei of helium-4 to make beryllium-8 (containing four protons and four neutrons) and then adding a further nucleus of helium to generate carbon-12 (containing six protons and six neutrons). However, beryllium is quite unstable, and can be expected to break apart into two nuclei of helium in 10-16seconds. On occasion, prior to the breaking apart of beryllium, a third helium nucleus collides with beryllium, resulting in a carbon nucleus. As it happens, the carbon atom possesses a special quantum property called a resonance, which facilitates this process. A resonance describes the discrete energy levels at which protons and neutrons in the nucleus can exist. Indeed, it turns out that the resonance of the carbon atom just so happens to correspond to the combined energy of the beryllium atom and a colliding nucleus of helium.

As Geraint Lewis and Luke Barnes explain, “if there were a resonance at just the right place in carbon, the combined energy of the beryllium and helium nuclei would result in a carbon nucleus in one of its excited states. The excited carbon nucleus knows how to handle the excess energy without simply falling apart. It is less likely to disintegrate, and more likely to decay to the ground state with the emission of a gamma-ray photon. Carbon formed, energy released… success!”5 Without this specific resonance level, the universe would contain relatively few carbon atoms — in 1953, this specific resonance that had previously been predicted by Fred Hoyle was discovered by William Fowler, precisely where Hoyle had predicted it would be.

A Remarkable Coincidence

This special carbon resonance (known as the Hoyle state), which corresponds to the energy levels of the combined beryllium-8 nucleus and a helium-4 nucleus, renders the otherwise improbable process of carbon-12 formation feasible and efficient in the high-temperature environments of stellar cores. This delicate balance of energy levels is a remarkable aspect of nuclear astrophysics that allows for the creation of the elements necessary for life. If it were not for this special resonance, life very probably would not exist in our universe. This is another one of many countless features of our universe that have to be “just right” for life — in particular, advanced life — to exist.

Notes

Kevin W. Plaxco and Michael Gross. Astrobiology: A Brief Introduction, 2nd edition (The John Hopkins University Press, 2011), chapter 1.

Primo Levi, The Periodic Table (Abacus, 1990), 226-227.

Robert E.D. Clark, The Universe: Plan or Accident? 3rd edition, (Zondervan, 1972), 97.

Kevin W. Plaxco and Michael Gross. Astrobiology: A Brief Introduction, 2nd edition (The John Hopkins University Press, 2011), chapter 1.

Geraint F. Lewis and Luke A. Barnes, A Fortunate Universe: Life in a Finely Tuned Cosmos (Cambridge University Press, 2017), 116-117.

Loving the little guy to death?

 

Thoughtful Darwinism to ID :lets be frenemies.

 A Secular Gay Agnostic Talks with Stephen Meyer

David klinghoffer

People who understand intelligent design and sympathize with it are a whole lot more diverse than ID critics assume. As I wrote here the other day about the “catholicity” or universalism of intelligent design:

Jewish theologian Will Herberg wrote a famous study of American society in 1955, Protestant, Catholic, Jew. Of course, that title left some important groups out. If I were going to write a book characterizing the universality of what we do, I might call it Protestant (Conservative or Liberal), Catholic, Jew, Eastern Orthodox Christian, Muslim, Agnostic, Platonist, Aristotelian. For David Berlinski, we might have to come up with a new category, “Enigmatic.” 

A Thoughtful History

Right on cue, there comes along secular gay agnostic writer David Moulton, with a thoughtful history and evaluation of the ID research project, including an interview with Stephen Meyer. Writing for Compact, the online magazine edited by Sohrab Ahmari, Moulton has read Meyer’s work carefully, along with that of Michael Behe, and he has studied the relevant history. He talks about Darwin’s Black Box, the Sternberg affair, Dover, scientism, Darwin’s Doubt, and much more. 

From, “Two Cheers for ‘Intelligent Design’”:

As an agnostic, I don’t accept all of Meyer’s conclusions. Nonetheless, it was refreshing to hear someone speak with so much rigor and erudition on the deepest questions of the human condition. He isn’t one to dodge hard problems or accept the arbitrary boundaries of academic specialization. Whether or not you agree with him, he offers provocative insights into science, philosophy, and the history of ideas.

So Moulton is not an ID advocate, but a sympathizer. I don’t see, though, why an agnostic couldn’t accept the conclusions of ID, and that first sentence of his above makes it sound like that’s what is holding him back. It need not deter him. An agnostic might recognize the scientific evidence but be unsure of the source of the design behind nature, while repeating Hamlet’s words, “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.”

Surprised by Scientism

He concludes poignantly with a recollection of his youth, and how he was taken by surprise by the rise of scientism:

As a teenager, I had no way of foreseeing these developments. All I knew was that I didn’t want to live in a society controlled by Christian fundamentalists. To this day, I believe in the fragile ideal of a secular, pluralistic society. I used to think that scientific expertise could help sustain this ideal by combating religious dogma. However, it’s clear by now that those who purport to speak in the name of science aren’t as neutral and objective as I once assumed. Often, science’s would-be spokesmen are bent on imposing their own dogmas. In hindsight, I should have been more concerned about scientism becoming an official state ideology. Science has many impressive discoveries to its credit, but we shouldn’t let it think and make political decisions on our behalf. Nor ought we to uncritically adopt the metaphysical views of the majority of scientists as our own. The question of God’s existence, for instance, remains as open today as at any other time in human history.  

Why, by the way, do I tick off Moulton’s identities in the headline? I hate putting people into simplistic categories (secular, gay, agnostic). I also hate thinking according to one’s tribe (“What is someone like me supposed to think?”), and I love it when people shatter stereotypes. A writer like Moulton is not supposed to “get” ID, but he does. Definitely read the rest at Compact (it’s behind a paywall).

Yet more on searching for a place like home.

 

The foundation of a living ecosystem vs. Datwinism

 An Astonishing Life-Friendly Coincidence: The Properties of the Nonmetal Atoms

Jonathan McLatchie

Arguably the strongest class of evidence for a cosmic designer is teleological arguments. It is well established that there are far more ways in which the universe might have been that are non-conducive to life than there are life-friendly ways. Given an assumption of theism, it is not particularly surprising that the universe would be hospitable to embodied conscious beings like ourselves. Given an assumption of atheism, conversely, it is wildly surprising that the universe would be supportive of such beings. In light of this significantly top-heavy likelihood ratio, the astronomical rarity of life-friendly universes (and the fact that our universe in fact does support advanced life) tends to confirm theism. One species of teleological argument that deserves more attention is the argument from the prior environmental fitness of nature for the existence of advanced life, which has been popularized in recent years by the work of Michael Denton. Cumulatively, the evidence adduced in Denton’s various books make for a very compelling case that a mind is behind the design of our universe.

Nonmetal Atoms Give Molecules with Shape

One subclass of evidence in this category is the apparent fine-tuning of chemistry for the carbon-based cell, of which you can read in The Miracle of the Cell, by Dr. Denton.1 Here, I will highlight just one example. The figure below shows the periodic table of elements

The elements colored purple in the figure represent the nonmetal atoms, and it is these that make up the material substances of the cell — in particular, carbon, hydrogen, oxygen, and nitrogen. These are in fact the only atoms that could be used to build a biochemical system since they can form strong, stable, directional chemical bonds. Critically, these covalent bonds give molecules with shape, and it is shape that is the essence of biochemistry. 

The Hydrophobic Force

Moreover, these atoms have an electronegativity such that the attraction of electrons for hydrogen and carbon is very similar. Since carbon and hydrogen have a similar value of electronegativity (i.e., how strongly atoms pull electrons towards the nucleus), this means that they are able to share electrons equally between the two atoms, creating a nonpolar covalent bond. On the other hand, when oxygen and hydrogen form a covalent bond, you get a polar molecule, where the electrons are shared unequally (specifically, oxygen has a higher electronegativity value, and hence attracts the shared electrons in the bond more strongly than does hydrogen).

This is critical for the whole organization of the cell, because it gives you the hydrophobic force, which is responsible for organizing the higher structure of the biological realm. The hydrophobic force refers to the tendency of nonpolar substances to aggregate in an aqueous environment to minimize their exposure to water. What causes this effect? When nonpolar molecules are introduced into water, it disrupts the structured hydrogen bonding network of water. Water molecules are unable to form hydrogen bonds with nonpolar molecules, leading to an energetically unfavorable situation. To minimize this disruption, water molecules arrange themselves in such a way that they are able to maintain as many hydrogen bonds as possible. To reduce the entropic cost and increase the overall stability, nonpolar molecules tend to aggregate together. By clustering in this way, the surface area in contact with water is minimized, and this reduces the number of water molecules that need to reorganize around them. For this reason, non-polar molecules are also called “hydrophobic” (water-repelling), whereas polar molecules are called “hydrophilic” (water-attracting).

The hydrophobic force is crucial to the assembly of membranes and proteins. Biological membranes are made up of phospholipids, which possess hydrophilic heads and hydrophobic tails. The hydrophobic tails avoid contact with water, whereas the hydrophilic heads interact with it. The result is the self-assembly of the phospholipids into a bilayer with the tails facing inward and the heads facing outward. In like manner, in a protein structure, amino acid side chains that are hydrophobic tend to avoid contact with the aqueous environment. On the other hand, chemical groups associated with polar (hydrophilic) side chains such as hydroxyl (-OH), amine (-NH2) and carboxyl (-COOH) groups form hydrogen bonds with water. The hydrophobic force drives the nonpolar residues to the protein’s interior, while the polar residues are exposed on the surface, interacting with water. This leads to the spontaneous folding of the protein into its native three-dimensional structure, which is crucial for its function.

So crucial is the hydrophobic force to protein folding that biochemist Charles Tanford, describing the discovery of how proteins fold, notes that “[T]he hydrophobic force is the energetically dominant force for containment, adhesion etc., in all life processes… This means that the entire nature of life as we know it is a slave to the hydrogen bonded structure of liquid water.”2

The Hydrophobic Force

Moreover, these atoms have an electronegativity such that the attraction of electrons for hydrogen and carbon is very similar. Since carbon and hydrogen have a similar value of electronegativity (i.e., how strongly atoms pull electrons towards the nucleus), this means that they are able to share electrons equally between the two atoms, creating a nonpolar covalent bond. On the other hand, when oxygen and hydrogen form a covalent bond, you get a polar molecule, where the electrons are shared unequally (specifically, oxygen has a higher electronegativity value, and hence attracts the shared electrons in the bond more strongly than does hydrogen).

This is critical for the whole organization of the cell, because it gives you the hydrophobic force, which is responsible for organizing the higher structure of the biological realm. The hydrophobic force refers to the tendency of nonpolar substances to aggregate in an aqueous environment to minimize their exposure to water. What causes this effect? When nonpolar molecules are introduced into water, it disrupts the structured hydrogen bonding network of water. Water molecules are unable to form hydrogen bonds with nonpolar molecules, leading to an energetically unfavorable situation. To minimize this disruption, water molecules arrange themselves in such a way that they are able to maintain as many hydrogen bonds as possible. To reduce the entropic cost and increase the overall stability, nonpolar molecules tend to aggregate together. By clustering in this way, the surface area in contact with water is minimized, and this reduces the number of water molecules that need to reorganize around them. For this reason, non-polar molecules are also called “hydrophobic” (water-repelling), whereas polar molecules are called “hydrophilic” (water-attracting).

The hydrophobic force is crucial to the assembly of membranes and proteins. Biological membranes are made up of phospholipids, which possess hydrophilic heads and hydrophobic tails. The hydrophobic tails avoid contact with water, whereas the hydrophilic heads interact with it. The result is the self-assembly of the phospholipids into a bilayer with the tails facing inward and the heads facing outward. In like manner, in a protein structure, amino acid side chains that are hydrophobic tend to avoid contact with the aqueous environment. On the other hand, chemical groups associated with polar (hydrophilic) side chains such as hydroxyl (-OH), amine (-NH2) and carboxyl (-COOH) groups form hydrogen bonds with water. The hydrophobic force drives the nonpolar residues to the protein’s interior, while the polar residues are exposed on the surface, interacting with water. This leads to the spontaneous folding of the protein into its native three-dimensional structure, which is crucial for its function.

So crucial is the hydrophobic force to protein folding that biochemist Charles Tanford, describing the discovery of how proteins fold, notes that “[T]he hydrophobic force is the energetically dominant force for containment, adhesion etc., in all life processes… This means that the entire nature of life as we know it is a slave to the hydrogen bonded structure of liquid water.”2

A Fortuitous Coincidence

It is thus a remarkably fortuitous coincidence that the very atoms that yield stable, defined shapes (from which macromolecules can be built) also generate the hydrophobic force which is the key to assembling them into higher three-dimensional forms. Nature does not owe us this life-friendly convergence, and yet if it were not for this coincidence, life could not exist. This is but one of many similar coincidences that are crucial to the existence of life — and, in particular, advanced life. Cumulatively, the evidence suggests that the universe was designed with life in mind.

Notes

Michael Denton, The Miracle of the Cell (Discovery Institute Press, 2020).

Charles Tanford, “How Protein Chemists learned about the Hydrophobic Factor: Protein Chemists and the Hydrophobic Factor.” Protein Science, vol. 6, no. 6, 1997, 1358-1366.

The King James Bible: a brief history.

 

Still yet another clash of titans.

Against ninsnevem ad pluribus XVI

 

Nincs:If it were not stated in the NT that Christ really died, and it were not in it that the Son was "the firstborn from/among the dead" (with 'ek'), then it would certainly be reasonable to argue that he never died and "the the firstborn OF the dead" (without 'ek') would not prove the opposite. The term "firstborn" (prototokos) in contexts such as "firstborn from the dead" implies both participation and preeminence. Christ was part of the dead and the first to be raised, underscoring His supremacy. But the notion that Christ would be created, or that He would be a creature, or that He would be connected to creation with "ek" is *nowhere* in the NT.

Me:more argument by assertion their is no ex at revelation ch.1:5,it's almost as if JEHOVAH Looked ahead and anticipated trintarian trickery here. Your argument by unfounded assertion proves nothing this time either .there is no need for any ex as plainly demonstrated by all the other uses of prototokos in scripture with or without the "ex" the prototokos is part of the implicit or explicit set . You proved utterly unable to put up re:an example from scripture yet you won't shut up you're just wrong here.

 In the Scripture the use of birth language re:JEHOVAH Is a reference to his creative activity 

   Hebrews ch.5:5So also Christ did not glorify Himself to become High Priest, but it was He who said to Him:

“You are My Son,

TODAY I have begotten You.”"

 The resurrection is a recreation of the one who has returned to his pre-creation state hence it us called begetting so Christ was begotten in time.

JEHOVAH of course had no recreation state hence cannot die and hence cannot be raised from the dead.

  Both of the Logos begettings were in time and were the result of his God's creative activity.

John ch.1:18LSB"No one has seen God at any time; the only begotten God who is in the bosom of the Father, He has explained Him."

The Logos is not merely a created person but a created God.

Note that the angels are called elohim

at psalms 8:5

Nincs:Your example about David also does not refute my position, according to which "firstborn of X" is not an inherently partitive structure, but whether the classification has taken place or whether the given concept conceptually requires membership is what decides it. It is not possible to be a pre-eminent king without being a king, but it is indeed possible to be a pre-eminent, distinguished heir being in a supreme position in relation to the whole creation, without being a creature.

Yes it is always necessary for the heir to be part of the family always your argument by unfounded assertion never works nincs never, we are supported by the TOTALITY of scriptural precedent and you continue to FAIL to demonstrate otherwise all you have to your back is wishful thinking.

For abiogenesis it's not so much uphill as up cliff.

 

How to write the next great novel?