Wednesday, 3 January 2024
Yet more on why "junk DNA" is junk no more.
Casey Luskin On Junk DNA’s “Kuhnian Paradigm Shift”
Prevailing scientific assumptions often die hard, especially when they fit so neatly into an evolutionary view of the development of life on Earth. On a new episode of ID the Future, Dr. Casey Luskin gives me an update on the paradigm shift around the concept of “junk DNA.”
Luskin explains that intelligent design theorists have long argued against the idea that non-protein coding DNA is useless evolutionary junk, instead predicting that it serves important biological functions. Year after year for over a decade, new evidence has emerged revealing such functions and vindicating ID scientists. Luskin summarizes several recent papers that have found specific functions for non-coding DNA, such as regulating gene expression, controlling development, and influencing epigenetic processes. He then reports on the latest new evidence: the function of short tandem repeats (STRs), previously considered “junk DNA.” Luskin also discusses the work of molecular biologist John Mattick, who has written recently about the shift in thinking about “junk DNA.” Luskin suggests a new way of looking at non-protein coding regions of DNA and concludes that, far from junk, these “highly compact information suites” are essential and serve a variety of important functions in the genome. Download the podcast or listen to it here
Technology is more predictive re:biology than physics?
Paper Digest: Standard Engineering Principles as a Predictive Framework for Biology
In 2017, professor of engineering Gregory T. Reeves and engineer Curtis E. Hrischuk published an open access paper in Journal of Bioinformatics, Computational and Systems Biology titled “The Cell Embodies Standard Engineering Principles.” They explained how the cell fulfills different sets of standard engineering principles (SEPs). This paper builds on Reeves and Hrischuk’s earlier publication that surveyed engineering models for systems biology. Once more these authors argue that engineering concepts can be used as a predictive and successful framework for biology.
Human designing and building have resulted in lists of standard engineering principles which must be followed to produce efficient, robust systems. These principles have been refined through countless engineering projects, and Reeves and Hrischuk demonstrate that these same SEPs are used in biology. They are therefore useful to biologists as an expectation framework for anticipating cellular systems:
The presence of engineering principles within the cell implies that SEPs can be used as starting point to formulate hypotheses about how a cell operates and behaves. In other words, we should pragmatically approach the cell as an engineered system and use that point of view to predict (hypothesize) the expected behavior of biological systems. We call this approach the Engineering Principle Expectation (EPE).
Several Categories of SEPs
In the paper, several categories of SEPs are examined: general engineering principles (GEPs), hardware/software codesign principles (CDEPs), and robotic engineering principles (REPs). For each of these categories, the authors give specific examples of how the cell conforms to the set of SEPs. The authors also develop a non-exhaustive list of SEPS for chemical process control engineering (CPCEP), since a list was not available.
The comparison between cellular systems and engineered systems has strong implications for intelligent design. The reality that cells abide by the same engineering principles discovered in human design is highly significant. This finding is much better predicted on the hypothesis that biological systems have been intelligently designed than the alternate theory of a blind neo-Darwinian process giving rise to living systems.
For the category of general engineering expectations, the authors go over three principles in the main text. GEP1 states that the “development of engineered objects follows a plan in accordance with quantitative requirements.” The authors point out that the development of molecular machinery requires careful orchestration, including but not limited to decision-making, gene expression, protein synthesis, post-translational modification, the assembly of multicomponent complexes, and life cycle processes like cell division. Thus, cells embody GEP1. GEP2 states that “requirements are ranked according to cost effectiveness, and the development plan, which has an incremental structure, emphasizes the higher-ranked requirements.” This principle describes hierarchy, which results from top-down design where components are constructed, and resources expended in accordance with higher system goals. To give a biological example, the authors note the prioritization of ATP in the cell. GEP3 states that “standards are used where available and applicable with every departure from applicable standards explicitly justified.” Biological examples include how all different types of cells have conserved features such as the genetic code, ATP, a near universal central metabolism. Amino acids, nucleic acids, and some lipids might all be thought of as a cellular standard from which deviations rarely occur.
Hardware/Software Co-Design Principles
Next the authors discuss hardware/software co-design principles starting with CDEP1. This is the principle of “partitioning the function to be implemented into small interacting pieces.” In the cell, cellular regulatory networks can be decomposed into autonomous acting modules which cooperate to accomplish a function. Even the basics of cellular physiology, where unique macromolecular structures such as chromosomes, membranes, and ribosomes exist, implies partitioning of function into small interacting pieces. Thus, cells abound with examples of autonomous players carrying out a specific role towards a greater purpose. CDEP2 is the principle of “allocating those partitions to microprocessors or other hardware units, where the function may be implemented directly in hardware or in software running on a microprocessor.” This principle underlies the benefit of having a separate processer for each function. In computer systems, manufacturing constraints preclude this from being possible, but the authors point out that the cell is able to realize the ideal of having each protein or complex operating independently as a unique unit of hardware.
Reeves and Hrischuk then describe REPs and CPCEPs. While going over each of those is beyond the scope of this article, the takeaway is that SEPs provide logic for understanding biological systems. By familiarizing themselves with these principles, biologists can enhance their research methodologies and improve their ability to predict and validate their experiments.
The Engineering Principle Expectation
Reeves and Hirschuk say that any complex system must adhere to SEPs. If it doesn’t, the outcome is catastrophic. Biological systems, which are more complex than any engineered system today, are not exceptions. When looking at a biological system, one should expect engineering characteristics. This can be thought of as the engineering principle expectation, a predictive model that can be used when looking at a biological system whose mechanistic details are not understood. Reeves and Hrischuk argue that it is crucial to apply engineering principles to understand and analyze biological systems. By doing so, researchers can gain insights into the underlying mechanisms and predict the behavior of these systems. Additionally, considering engineering principles can help in designing effective interventions or therapies for complex biological problems.
Theistic Darwinism is not an oxymoron? II
Could Finely Tuned Initial Conditions Create Biological Organisms?
Is the arrangement of mass energy at the beginning of all things sufficient to account for the origin of life, the diversification of life, our capacity for abstract thought, volition, spiritual communion, and more? At present, there seems to be very little reason to answer in the affirmative.
However, theologian Rope Kojonen, in an attempt to wed design and evolution, allows for this interpretation in his recent book, The Compatibility of Evolution and Design. My colleagues and I reviewed the book in the journal Religions and have been discussing it further in a series here. The laws and preconditions of nature are at the heart of Kojonen’s model. They are his proposed mechanisms of design, the linchpin of his project. Yesterday, we looked at the first of three interpretations of how Kojonen’s model would actually work. Today we will look at the second:
The laws of nature simply transmitted biologically relevant information sufficient to produce all biological complexity and diversity, including new proteins, protein machines, and the like. This biologically relevant information was “built in” to the mass-energy configuration at the Big Bang. The laws of nature did not create anything but rather were the media (or “carriers”) through which biologically relevant information was eventually expressed and instantiated in everything from proteins to bacterial flagella to human beings.
A Helpful Analogy
Laws have the capability of transmitting information in some situations, but they lack the ability to generate biological information of the kind found in DNA and proteins, as we’ve already discussed. Philosopher of science Stephen Meyer develops this point with a helpful analogy in Return of the God Hypothesis:
[I]magine that a group of small radio-controlled helicopters hovers in tight formation over the Rose Bowl in Pasadena, California. From below, the helicopters appear to be spelling a message: “Go USC.” At halftime, with the field cleared, each helicopter releases either a maroon or gold paint ball, one of the two University of Southern California colors. Gravity takes over and the paint balls fall to the earth, splattering paint on the field after they hit the turf. Now on the field below, a somewhat messier but still legible message appears. It also spells “Go USC.”
Did the law of gravity, or the force described by the law, produce this information? Clearly, it did not. The information that appeared on the field already existed in the arrangement of the helicopters above the stadium in “the initial conditions.” Gravitational forces played no role in causing the information on the field to self-organize. Gravity merely transmitted preexisting information from the helicopter formation to the field below.
The information in the message was encoded in the original position of the helicopters. The laws of nature (and gravity in particular) were merely the “carrier” of this previously created information. The second interpretation of Kojonen’s view agrees with this perspective of the laws of nature but then supposes that all the information necessary for the origin of life, diversification of life, and accounting for human cognition was present in the initial conditions (positioning of matter and energy). This concept is comparable to playing pool, where a single strike of the cue ball can knock all the balls into their respective holes due to their positions on the table. This mechanism is highly implausible when applied to life because the initial conditions that would have had to be established to create such a system are extreme.
Six Objections from Meyer
Additional problems plague this “initial conditions” idea. In Return of the God Hypothesis, Meyer summarizes six objections.
[G]iven the facts of molecular biology, the axioms of information theory, the laws of thermodynamics, the high-energy state of the early universe, the reality of unpredictable quantum fluctuations, and what we know about the time that elapsed between the origin of the universe and the first life on earth, explanations of the origin of life that deny the need for new information after the beginning of the universe clearly lack scientific plausibility.
Let’s explore this a bit more. To understand the absurdity of proposing that initial conditions could, without additional intervention, account for the facts of molecular biology, consider again the pool analogy. The idea that unfavorable thermodynamic events could be stacked into the initial conditions would be like supposing that after the cue ball hit one ball, three balls went in immediately, but after ten minutes, three more went in, and finally all the balls went into the holes. This scenario is scientifically implausible because our experience with the laws of nature is that they work consistently through time, and only agents that can work outside of the system are able to cause new events to occur. Thus, after a causation event, processes that must overcome thermodynamic barriers do not occur.
An Unknown Force in History
While the laws of nature can transmit information, the way they transmit it is consistent and constant. If the initial conditions could do something thermodynamically unfavorable after time has elapsed from an initial agent’s action, this would certainly be different from what we observe today. The laws would require the ability to select specific outcomes — i.e., to assemble specific molecules into these outcomes at specific points in time. This would require a process model running in the background and invoking the right actions at the right times — an unknown force that only seems to work at specific times in history.
Tomorrow, we will look at the final possible interpretation of Kojonen’s model for the laws of nature.
Tuesday, 2 January 2024
Theistic Darwinism is not an oxymoron?
Physics and Chemistry Could Not Give Rise to Biology
The laws of nature provide stable conditions and physical boundaries within which biological outcomes are possible. Laws are, in effect, a chessboard. They provide a stable platform and non-negotiable boundaries. But they do not determine the movement of pieces or the outcome of the game.
Or do they? Rope Kojonen, a theologian at the University of Helsinki, argues for the compatibility of design and evolution. My colleagues Steve Dilley, Brian Miller, Casey Luskin, and I published a review of Kojonen’s thoughtful book, The Compatibility of Evolution and Design, in the journal Religions. In a series at Evolution News, we have been expanding on our response to Dr. Kojonen. Here, I will shift gears to analyze his claims about the laws of nature and their role in the origin of biological complexity and diversity.
Mechanisms of Design
The laws of nature are at the heart of Kojonen’s model. They are the mechanisms of design, the linchpin of Kojonen’s project to wed design and evolution. To evaluate his model, however, we need to be clear about what exactly his position is. Kojonen is not entirely clear about how the laws of nature (and initial conditions) are said to bring about the origin of life, the diversification of life, and human cognition. However, there seem to be at least three possible ways to interpret Kojonen’s model:
The laws of nature gave rise to “laws of forms” and other preconditions, which allowed selection and mutation (along with other processes) to create all biological complexity and diversity, including nucleotide sequences, new proteins, the assembly of protein machines, intricately engineered motility, and navigation systems, and all the unique capabilities possessed by humans. In this view, the laws of nature (in the main) have causal power or limit the possibility space enough that organisms emerge. Notably, this process isn’t deterministic per se. On this interpretation, there is room for environmental conditions to work alongside laws of nature to shape what evolutionary pathways are available, what kind of structures are easier to evolve, and so on. Insights from structuralism, convergence, and evolutionary algorithms apparently provide details about how this might work. But, the bottom line with this interpretation is that the laws of nature and environmental conditions play a generative role in bringing about flora and fauna. The laws of nature, environmental conditions, and so on don’t simply transmit biologically relevant “information” built into the initial conditions of the Big Bang. Instead, they actually create more biologically relevant information.
The laws of nature simply transmitted biologically relevant information sufficient to produce all biological complexity and diversity, including new proteins, protein machines, and the like. This biologically relevant information was “built in” to the mass-energy configuration at the big bang. The laws of nature did not create anything but rather were the media (or “carriers”) through which biologically relevant information was eventually expressed and instantiated in everything from proteins to bacterial flagella to human beings.
The laws of nature gave rise to “platonic” forms, which then constrained evolution in ways that allowed selection and mutation to build biological forms. These “forms” are “an emergent consequence of the laws of chemistry and physics.” In this interpretation, the laws created these forms. The forms themselves are more than simply laws and matter under a different guise; they are non-physical. In this view, laws generated these forms, which then shaped the physical tendencies of matter such that (with possible contingency and other factors in play) they produced biological information sufficient for selection and mutation to evolve all manner of proteins, protein machines, unique human abilities, and the like.
Let’s discuss point one, namely, that the laws of nature (and the like) have causal power or limit the possibility space enough that the diversity of plant and animal species observed today emerged from unicellular organisms. While I am personally convinced that design is evident in the very fabric of the universe and yes, in the laws of physics and chemistry, these material mechanisms do not have sufficient causal power or limit the possibilities sufficiently to explain how the diversity of organisms came to be (if these laws have stayed the same over time). To support this point, I’ll talk about the capabilities of the laws of physics and chemistry and give examples of how they currently interact with biology.
In Kojonen’s model, the laws of nature do the heavy lifting in terms of creating biological complexity. While Kojonen cites an array of other factors — e.g., environmental conditions, structuralism, convergence, and evolutionary algorithms — it’s also clear that these factors are undergirded by the laws of nature themselves. But there are limits to the creative power of the laws of nature. If it turns out that the laws have limited ability to produce biological complexity, then other factors (such as the environment, convergence, etc.) that depend upon the laws of nature likewise have limits. If Kojonen thinks that these other factors have creative powers that transcend the limits of the laws of nature, then the burden is on him to show that. Is it possible for the laws of nature to be a causal force or sufficiently constrain the possibility space?
Material Mechanisms
According to one definition, a mechanism is a process that acts on objects to produce an outcome. Here I will define a material mechanism as a process by which a physical object is acted upon by one of the physical laws. Material objects are built from the elements of the periodic table, and the laws of physics and chemistry are the constant processes that constrain how material objects behave. To understand materialistic mechanisms, let’s look at a few illustrations.
The Law of Gravity
Definition: The law of universal gravitation says an object will attract another object proportionally to the product of their masses and inversely related to the square of their distance from each other.
This law tells us how objects behave toward one another. Gravity constrains motion, whether that motion is human, planetary, or light. A complex system may also be able to detect gravity and use it as a cue. Let’s look at an example of plant growth. Leaves grow in the opposite direction of gravitational pull, but roots grow downward in the direction of gravitational pull. What causes this? Is it gravity? Definitely not. Root growth occurs through the division of stem cells in the root meristem, located at the tip of the root. Thus, root stem cells rely on gravity as a cue to be detected by their sensors, so that they know where to direct their growth. But gravity is not the mechanism that creates plant morphology. Rather, plants work within the constraints of gravity and exploit it via sensors to scaffold their architecture.
Electrostatic Laws
Definition: The electrostatic laws state that charges attract or repel with a force that is proportional to the product of their charges and inversely proportional to the square of the distance between them, depending on whether they are alike or different.
Electrostatic laws describe the attraction of positively charged ions to negatively charged ions. These laws constrain (but do not cause) the way an electrochemical gradient can be formed and work across a membrane. The charge and concentration differential across a membrane creates an electrical field. The cell then uses the potential energy of the electrical field to generate energy, convey electrical signals, and power the delivery of nutrients into the cell. The crucial point here is that electrochemical gradients are not an emergent property of the electrostatic laws. Instead, they are caused by molecular machinery. As Elbert Branscomb and Michael J. Russell say in a recent BioEssays paper, “to function, life has to take its transformations out of the hands of chemistry and operate them itself, using macromolecular “mechano-chemical” machines, requiring one machine (roughly) for each transformation; life must, in Nick Lane’s evocative phrasing, “transcend chemistry.” (Branscomb and Russell 2018)
How do electrostatic laws interface with organisms’ body plans? Organism body patterning is formed in part by bioelectrical networks, which operate across cell fields to integrate information and mediate morphological decision-making. (Djamgoz and Levin 2022) The bioelectrical networks play critical roles by regulating gene expression, organ morphogenesis, and organ patterning. This is, of course, exactly what would be necessary as an emergent property from electrostatic laws for them to have generative capacity. But these bioelectric networks no more emerge from the electrostatic laws than do cellular networks; rather, these bioelectric networks are information rich networks which carry information in a bioelectric code which can be understood by the sender and receiver. (Levin 2014)
The Periodic Table of Elements
Now the electrostatic laws, in conjunction with the design of the periodic table of elements, constrain the possible chemical space of molecule bonding arrangements. For example, based on the chemical characteristics of hydrogen and oxygen as well as the electrostatic laws, H2O has a specific bonding configuration. These mechanisms can thus explain the origin and ready formation of some simple molecules. But what about more complex molecules like those used in life? According to a paper in the journal Nature, “Chemical space and biology,” “The chemical compounds used by biological systems represent a staggeringly small fraction of the total possible number of small carbon-based compounds with molecular masses in the same range as those of living systems (that is, less than about 500 daltons). Some estimates of this number are in excess of 1060.” (Dobson 2004) This statement is consistent with our observation that complex molecules like glucose and nucleic acids result from enzymes. If one thinks that electrostatic laws and the periodic table limit the search space so that molecules like nucleic acids form on their own, then nucleic acids should form spontaneously from phosphate, nitrogen, carbon, hydrogen, and oxygen, just like water does. But this is not something that is observed. Instead, complex molecules in an appreciable quantity can only be built using enzymes (which are built using information in DNA) or in highly controlled laboratory synthesis environments. Not to mention the fact that there must be something in the natural laws that “forces” the chemistry of life to use only left-handed molecules. And if that is true, then why aren’t all molecules left-handed as this would seem to require a “rule” in the laws.
If one grants the first cell (supposing the origin of life is a miraculous event), there remain thousands of unique molecular compounds essential for the diversity of life to be selected from the chemical space. We know that many of these molecular structures are multipurpose, recyclable, and essential to other ecosystem members. The design of these molecules and the enzymes that make and break them down appears to have required foresight for the needs and functions of the ecosystem as well as an in-depth understanding of chemistry and biochemistry. Is this type of information and causal power available in the electrostatic laws or the other laws of nature?
Laws of Thermodynamics
Definition: The first law of thermodynamics says that matter and energy cannot be created or destroyed but can only change form. The second law of thermodynamics says that closed systems always move toward states of greater disorder. Open systems move toward equilibrium, where the disorder (aka entropy) of the universe is at its maximum.
The laws of thermodynamics place constraints on what biological organisms must do to remain alive. That is, organisms must capture, harness, and expend energy to maintain a state far from equilibrium. To do this, organisms must/do have incredibly designed architectures that reflect a highly advanced understanding and exploitation of the laws of nature. For example, in central carbon metabolism, energy is extracted from the molecule glucose in the most efficient way possible. But just because this biochemical pathway exhibits an architecture that is amazingly designed to leverage the constraints imposed by thermodynamics does not mean that the laws provide a mechanism by which these complex systems arose in the first place. In other words, simply because a vehicle is highly efficient does not imply that the laws of thermodynamics designed it. More likely, it means whoever designed the vehicle had a thorough understanding of thermodynamics.
Quantum Physics
Definition: Quantum physics describes the physical properties at the level of atoms and subatomic particles using the wave function, which is determined by the Schrödinger equation. The Schrödinger equation is the quantum counterpart of Newton’s second law, describing what happens in the quantum realm to systems of subatomic particles.
Schrödinger equations are linear equations, so when added, the outcome is also linear. This is very different from what is observed in the real world. For biology and complex systems, conditional branching occurs, as in the example:
If {antibiotic is detected} then (express antibiotic efflux pump). If {antibiotic decreases} then (decrease expression of antibiotic efflux pump).
This type of branching found in complex systems cannot be boiled down to a wave function. Thus, as George Ellis, a leading theorist in cosmology and complex systems, says “[T]here is no single wave function for a living cell or macroscopic objects such as a cat or a brain.” In short, the complex nonlinear world is unable to arise from a single wavefunction.
DESIRE TO SURVIVE — NOT A MATERIALIST MECHANISM
Definition: The behavior that an organism programmatically/cognitively undertakes to avoid death.
The laws of physics and chemistry do NOT include natural selection. Natural selection is an outcome of the programming of a specific goal: desire to survive. As such, I define natural selection as the change in populations that depends upon their programmed and, in some cases, cognitive capacity to survive and the environmental factors they face. Please note that this definition is different from how most people might think of natural selection, but one hopes it is more accurately aligned with how it actually works. To support this goal, the “desire to survive,” organisms have a variety of mechanisms that may include both voluntary and involuntary responses. For example, in humans, the immune system would be an example of an involuntary response (programmatically compiled) where the defenses of the body fight off invaders. An example of a voluntary response (a cognitive response) in humans might be when someone runs for their life from a bear or kills a poisonous snake. Another example of an involuntary mechanism is natural genetic engineering. In case you aren’t familiar with natural genetic engineering, it just means that cells have the capability to actively reorganize and modify their own genomes to enable survival. This involves mechanisms like transposition (movements of genetic elements within the genome), gene duplication, horizontal gene transfer (transfer of genetic material between different organisms), and other forms of genetic rearrangement. Another important example is phenotypic plasticity, which has frequently been confused for natural selection but is the ability of an individual organism to exhibit different phenotypes (observable characteristics or traits), for example, in response to changes it senses in the environment. Phenotypic plasticity occurs too rapidly to be driven by mutation and selection; thus, it is recognized as an innate adaptation algorithm embedded within an organism.
So, the desire to survive, coupled with environmental conditions and random mutations that favor some individuals over others, is “natural selection.” As natural selection relies on the agent- or life-specific mechanism of a desire to survive, it cannot account for anything related to the origin of life, only the diversification of life. The degree to which natural selection can account for the diversification of life is an active area of research, but ID proponents Douglas Axe and Brian Miller have discovered some important limits. Miller summarized decades of research on the topic of protein evolution, which relies on natural selection, in our response to Rope Kojonen. In short, they have shown that natural selection is not capable of creating a high-complexity enzyme from a random sequence of amino acids or of transforming one protein fold into a different fold without guidance. This is effectively an upper bound for what natural selection can accomplish, which bears not only on origin-of-life scenarios but also on the ability of life to diversify from a single organism into the diversity we see today.
Necessary but Not Sufficient
The emergent properties of physics and chemistry are necessary, but not sufficient to explain the origin or diversification of biological organisms. Gravity can be used as a cue by biology to determine directionality, but gravity doesn’t make a leaf grow up or a root grow down — that happens only because a complex system is sensing, interpreting, and acting on the gravitational cue. The design of the periodic table of elements constrains the bonding pattern between hydrogen and oxygen and bestows upon water its life-giving properties, but these constraints on chemical bonding do not cause the formation of DNA or other complex molecules. Enzymes are necessary for more complex molecules to be formed at the rate required for life. The electrostatic laws describe how positive and negative charges attract one another, but these laws do not cause the formation of an electrochemical gradient across a membrane — that only happens because molecular machines harness energy to push a system away from equilibrium. In quantum physics, the linear wave function describes the wave-particle duality of matter, but it cannot account for the conditional branching observed in complex systems.
In short, the best way to summarize the capacity of all these material mechanisms is in George Ellis’s words from his recent article, “Quantum physics and biology: the local wavefunction approach”: “The laws of physics do not determine any specific outcomes whatsoever. Rather they determine the possibility space within which such outcomes can be designed.” (Ellis 2023)
Tomorrow we will look at the second interpretation of Kojonen’s model for how the laws of nature and initial conditions could bring about life and its diversification.
John Ch.1:1 and the God of the Logos
John Ch.1:1George Lamsa translation"The Word was in the beginning, and that very Word was with (the) God, and God was that Word." Bracketts mine.
The God that the word was with is definitely a God. So if the word is truly his equal then he should also be a God but not the God he was with. Two co-equal Gods would be bitheism.
Note that although :John Ch.1:14GLT"And the Word became flesh,..."
The God he was with remained spirit.
John Ch.4:24GLT"For (not merely the Father but the)God is Spirit; and those who worship him must worship him in spirit and in truth."
ONLY the God and Father of Jesus is ever referred to as "ton theon"or "ho theos" the God indicating the most high God no one else. So the God and Father of Jesus is definitely a God which is in itself a falsification of the trinity dogma. As no member of the trinity can be a or the most high God in his own right. Yet the Bible repeatedly declare this to be the case of the God and Father of Jesus and NO ONE else.
Luke Ch.1:32GLT" He will be great, and he will be called the Son of the HIGHEST; and the LORD God will give him the throne of his father David."
Monday, 1 January 2024
Sunday, 31 December 2023
From the CBS news website on birthdays.
Why do we celebrate birthdays?
The idea of celebrating the date of your birth is a pagan tradition. In fact, many Christians didn't celebrate birthdays historically, because of that link to paganism.
Pagans thought that evil spirits lurked on days of major changes, like the day you turn a year older.
The ancient Greeks believed that each person had a spirit that attended his or her birth, and kept watch. That spirit "had a mystic relation with the God on whose birthday the individual was born," says the book The Lore of Birthdays.
• Why do we blow out candles on our birthday?
The candles were a response to the evil spirits. They showed up to communicate with the gods. A light, in the darkness.
Church Father origen against birthdays
.of all the holy people in the Scriptures, no one is recorded to have kept a feast or held a great banquet on his birthday. It is only sinners (like Pharaoh and Herod) who make great rejoicings over the day on which they were born into this world below (Origen, in Levit., Hom. VIII, in Migne P.G., XII, 495) (Thurston H. Natal Day. Transcribed by Thomas M. Barrett.
Saturday, 30 December 2023
Friday, 29 December 2023
Time travelling birds?
Fossil Friday: Fossil Bird Tracks Expand the Temporal Paradox
The origin of birds involves a severe problem for Darwinists, which paleo-ornithologist Alan Feduccia has called a temporal paradox (1994, 1996). The paradox lies in the fact that primitive fossil birds are contemporaneous with or even appear earlier in the fossil record than their assumed theropod dinosaur ancestors. This is the opposite of the natural expectations from a Darwinian point of view, and therefore has to be explained away with ad hoc hypotheses such as ghost lineages, which are long spans of existence of groups that leave no fossil record. Of course, Darwinists always hope that this problem will be solved with new fossil discoveries and many such claims have been made quite unsuccessfully as I have elaborated in previous articles (see Bechly 2022).
A New Discovery
Now, a new discovery published in the journal PLOS ONE may have made the notorious temporal paradox of birds even worse — much worse — because it extends the existence of bird-like forms many million years further into the past, preceding any of the less bird-like theropods.
Earlier this month, a team of scientists from the University of Cape Town (Abrahams & Bordy 2023) reported the identification of bird-like footprints from the Upper Triassic of Lesotho in southern Africa, which are at least 210 million years old. Actually, the fossil tracks were already discovered and described by paleontologist Paul Ellenberger in the mid 20th century and classified as ichnogenus Trisauropodiscus. The validity of this ichnogenus was later questioned by other scientists, and an avian affinity has been hotly debated. Abrahams and Bordy re-examined original field material, casts, historical photographs, and interpretative sketches in previous publications. Based on this revision they could identify “two distinct Trisauropodiscus morphotypes, one of which resembles footprints made by birds.” The authors discuss various criteria to distinguish the tracks of non-avian dinosaurs from bird-like dinosaurs ancestral to birds, and found several clear criteria of the second morphotype uniquely matching bird-like tracks. As commenter Nield (2023) readily admitted: “These footprints are something of a mystery: fossils for even the earliest bird ancestors don’t show up for another 60 million years.”
This new finding parallels the discovery of tetrapod tracks in the Zachelmie quarry in Poland, which turned out to be 10 million years older than even the oldest fishapod putative ancestors of quadrupedal land vertebrates such as the famous Tiktaalik or even the totally fish-like Eusthenopteron (Niedźwiedzki et al. 2010, Ahlberg 2019). Empirical data again conflict with Darwinian story-telling. In spite of the unique similarity with modern bird tracks, the researchers therefore speculated that the producer of the Trisauropodiscus tracks might have been some kind of three-toed archosaur with convergent bird-like pedal morphology. Consequently, the press release of the discovery says that “unknown animals were leaving bird-like footprints in Late Triassic Southern Africa” (PLOS 2023), and Smithsonian Magazine commented that “mysterious creatures with bird-like feet made these tracks long before birds evolved” (Kuta 2023). In the same spirit, another commenter (Yazgin 2023) asked “who made the footprints if the earliest known birds didn’t emerge until at least 50 million years later?” and answered: “Until the fossil of an animal that lived at the right time, in the right place, and with the right proportions is found, the mystery of who created the Trisauropodiscus tracks remains.”
Protecting the Evolutionary Narrative
To be clear: nothing in these fossil footprints themselves suggests that they are anything but bird tracks, but they have to reinterpreted as something else to protect the evolutionary narrative from inconvenient conflicting evidence and unsolved mysteries. Theory trumps data in evolutionary biology.
With this final Fossil Friday article for 2024, I wish everybody a happy New Year. I hope you will enjoy my articles in the coming year as well.
References
Abrahams M & Bordy EM 2023. The oldest fossil bird-like footprints from the upper Triassic of southern Africa. PLoS ONE 18(11): e0293021, 1–17. DOI: https://doi.org/10.1371/journal.pone.0293021
Ahlberg PE 2019. Follow the footprints and mind the gaps: a new look at the origin of tetrapods. Earth and Environmental Science Transactions of The Royal Society of Edinburgh 109(1-2), 115–137. DOI: https://doi.org/10.1017/S1755691018000695
Bechly G 2022. Fossil Friday: The Temporal Paradox of Early Birds. Evolution News August 19, 2022. https://evolutionnews.org/2022/08/fossil-friday-the-temporal-paradox-of-early-birds/
Feduccia A 1994. The Great Dinosaur Debate. Living Bird Quarterly 13(4), 28–33.
Feduccia A 1996. The Origin and Evolution of Birds. Yale University Press, New Haven (CT), 432 pp.
Kuta S 2023. Mysterious Creatures With Bird-Like Feet Made These Tracks Long Before Birds Evolved. Smithsonian Magazine December 4, 2023. https://www.smithsonianmag.com/smart-news/mysterious-creatures-with-bird-like-feet-made-these-tracks-long-before-birds-evolved-180983362/
Niedźwiedzki G, Szrek P, Narkiewicz K, Narkiewicz M, Ahlberg PE 2010. Tetrapod trackways from the early Middle Devonian period of Poland. Nature 463, 43–48. DOI: https://doi.org/10.1038/nature08623
Nield D 2023. Mysterious Bird-Like Footprints in Africa Predate The Existence of Birds. ScienceAlert December 4, 2023. https://www.sciencealert.com/mysterious-bird-like-footprints-in-africa-predate-the-existence-of-birds
PLOS 2023. Unknown animals were leaving bird-like footprints in Late Triassic Southern Africa. ScienceDaily November 29, 2023. https://www.sciencedaily.com/releases/2023/11/231129150127.htm (also see Phys.org)
Yazgin E 2023. Mysterious bird-like tracks in Africa: The oldest birds? Cosmos Magazine November 30, 2023. https://cosmosmagazine.com/history/palaeontology/oldest-bird-tracks-fossil-africa/
Thursday, 28 December 2023
The crisis continues says Michael Denton.
Biologist Michael Denton Revisits His Argument that Evolution Is a "Theory in Crisis"
Wednesday, 27 December 2023
Tuesday, 26 December 2023
Monday, 25 December 2023
Sunday, 24 December 2023
Hosea Chapter 1 American Standard Version
1.The word of JEHOVAH that came unto Hosea the son of Beeri, in the days of Uzziah, Jotham, Ahaz, and Hezekiah, kings of Judah, and in the days of Jeroboam the son of Joash, king of Israel.
2 When JEHOVAH spake at the first by Hosea, Jehovah said unto Hosea, Go, take unto thee a wife of whoredom and children of whoredom; for the land doth commit great whoredom, departing from JEHOVAH.
3 So he went and took Gomer the daughter of Diblaim; and she conceived, and bare him a son.
4 And JEHOVAH said unto him, Call his name Jezreel; for yet a little while, and I will avenge the blood of Jezreel upon the house of Jehu, and will cause the kingdom of the house of Israel to cease.
5 And it shall come to pass at that day, that I will break the bow of Israel in the valley of Jezreel.
6 And she conceived again, and bare a daughter. And JEHOVAH said unto him, Call her name Lo-ruhamah; for I will no more have mercy upon the house of Israel, that I should in any wise pardon them.
7 But I will have mercy upon the house of Judah, and will save them by JEHOVAH their God, and will not save them by bow, nor by sword, nor by battle, by horses, nor by horsemen.
8 Now when she had weaned Lo-ruhamah, she conceived, and bare a son.
9 And JEHOVAH said, Call his name Lo-ammi; for ye are not my people, and I will not be your God .
10 Yet the number of the children of Israel shall be as the sand of the sea, which cannot be measured nor numbered; and it shall come to pass that, in the place where it was said unto them, Ye are not my people, it shall be said unto them, Ye are the sons of the living God.
11 And the children of Judah and the children of Israel shall be gathered together, and they shall appoint themselves one head, and shall go up from the land; for great shall be the day of Jezreel.
On the right to conscientious objection
OHCHR and conscientious objection to military service
While the Covenant does not explicitly refer to a right to conscientious objection, in its general general comment no.22 (1993) the Human Rights Committee stated that such a right could be derived from article 18, inasmuch as the obligation to use lethal force might seriously conflict with the freedom of conscience and the right to manifest one’s religion or belief.
The Human Rights Council, and previously the Commission on Human Rights, have also recognized the right of everyone to have conscientious objection to military service as a legitimate exercise of the right to freedom of thought, conscience and religion, as laid down in article 18 of the Universal Declaration of Human Rights and article 18 of the International Covenant on Civil and Political Rights
Why the irrational atheist would be an atheistic society's only hope.
Every single time atheists have had the floor to themselves re:governance the result has been a mass murdering thugocracy. While the premise of atheism is irrational the social darwinism that the atheistic regimes of the 20th century have espoused is a perfectly rational conclusion given that premise as starting point.
In the atheistic universe there would be no reason to hope for anything else but the pitiless struggle between bloodlines for supremacy . Even among social animals suppression/culling of bloodlines that were a demonstrable liability to the herd would be rational. The preservation/promotion of bloodlines that were a proven asset to the herd would also be rational. Casting the matter in moral or ethical terms would be nothing but uninformed sentimentality.
Rather than looking to the sky and taking the altruistic generosity of a benevolent Father as an example . We should look to the Brute beast, after all their pitiless struggle for supremacy is the true source of our bounty.
We see no hang ups re: morality there. If a stronger herd must violently displace a weaker one to advance its aims so be it and neither the displacer nor the displaced thinks of the matter in moral terms, it is simply the way things are and there is no particular way things ought to be.
Even this arbitrary assignment of some special status to life itself would be an atavism from religion/superstition. There is only physics life/consciousness is an illusion, a very flattering illusion, hence its persistence, but really when one thinks of it there is no meaningful difference between living and nonliving matter and neither exists for any objective purpose.
All perfectly rational conclusions given atheism as a premise. Hence the irrational atheist would be an atheistic society's only hope.
Saturday, 23 December 2023
Another Friday another missing link (or not).
Fossil Friday: Is the Four-Legged Snake Tetrapodophis a Missing Link or Not?
The origin of snakes is a hotly debated topic in evolutionary biology. There are controversies about their phylogenetic position, their origin from aquatic vs burrowing (fossorial) ancestors, and of course transitional fossils (Caldwell & Lee 1997, Rieppel et al. 2003, Brandley et al. 2008, ApesteguÃa & Zaher 2006, Lee et al. 2007, Caldwell 2007, 2008, Zaher et al. 2009, 2023, Longrich et al. 2012, Zaher & Scanferla 2012, Palci et al. 2013a, 2013b, Palci 2014, Caldwell et al. 2015, Hsiang et al. 2015, Yi & Norell 2015, Da Silva et al. 2018, Xing et al. 2018, Garbergoglio 2019a, 2019b, 2019c). While some scientists are convinced that “snakes and mosasauroids/coniasaurs share a limbed common ancestor that was likely aquatic, not fossorial” (Caldwell 2008), other scientists strictly claim that “lizards could not have transitioned to snakes by any other evolutionary path than through fossoriality” (Da Silva et al. 2018). Either way, there should have existed transitional forms, which exhibit at least some typical features of basal snake anatomy combined with four fully developed fore and hind limbs to document the transition of limbless snakes from still quadrupedal walking ancestors.
Assumed Mesozoic stem snakes like the Madtsoiidae and Simoliophiidae as well as the very primitive Cretaceous genera Coniophis, Dinilysia, and Najash did only possess small external hind limbs (of which vestigial remnants are also retained in some living snakes like boids), but show no evidence of forelimbs (Tchernov et al. 2000, Zaher & Rieppel 2002, Rieppel et al. 2003, ApesteguÃa & Zaher 2006, Garberoglio et al. 2019c).
In their study of the evolution of the snake body plan Garberoglio et al. (2019c) commented:
This basal position of the limbed terrestrial and marine snakes indicates that snakes retain sizeable external hindlimbs and sacral contacts for a substantial time after their origin—from approximately 170 Ma to the youngest confirmed legged snakes, the simoliophiids, at approximately 100 Ma. This indicates that (i) the reduction and loss of the pectoral girdle and forelimbs probably occurred much earlier, given the definitive absence of these structures in simoliophiids and the lack of evidence for their presence in Najash, Dinilysia, and madtsoiids, and was probably a major event in the early radiation of snakes, and one that occurred well before crown (modern) snake origins; (ii) the “forelimb-absent and hindlimb-reduced” morphology was a stable and successful body plan, rather than a transient phase between limbed and limbless conditions; and (iii) the origin of crown snakes was characterized by a major reduction in the hindlimb and pelvis (including loss of sacral contacts).
This All Sounds Well and Good
That is, until you find that other modern studies (e.g., Tchernov et al. 2000, Rieppel et al. 2002, Zaher & Rieppel 2002, Longrich et al. 2012, Zaher & Scanferia 2012, Palci et al. 2013b in part, Hsiang et al. 2015, Garbergoglio et al. 2019a contra Garbergoglio et al. 2019c) do not even agree that the fossil Madtsoniidae and Simoliophidae or even Dinilysia are stem group snakes at all, but recover them nested among living snakes, which would imply that the hind limb reduction occurred more than once in crown group snake. Probably, mainstream evolutionary biologists would respond that such a reduction is simple and therefore not unlikely, as is proven by the fact that several other groups of amphibians and reptilians have produced legless forms. However, this is exactly the point: convergence is all over the place in the animal kingdom and is nothing but incongruent similarity that contradicts a unique nested hierarchy of similarities predicted by Darwinism. Furthermore, there is experimental evo-devo evidence from transgenic mice that the reduction of limbs is not a simple task at all but requires multiple codependent mutations (compare Kvon et al. 2016). Together with the complex changes in skull kinetics of snakes, this raises a significant waiting time problem, because even the geologically available window of time of several million years is orders of magnitude too short to accommodate the genetic changes for this re-engineering of the body plan, based on the mathematical toolkit of mainstream population genetics.
Anyway, because of the fact that no known fossil stem snakes had retained four functional limbs, the discovery of a putative four-legged snake was a real sensation. Eight years ago my good colleague Prof. David Martill, with whom I co-authored several articles and monograph of the fossils of the Lower Cretaceous Crato Formation in Brazil (Martill et al. 2007), described from this locality the long sought missing link of snake evolution in the prestigious journal Science (Martill et al. 2015; also see this YouTube video): the beautifully and completely preserved fossil shows a very elongate snake-like animal with small fore and hind limbs, both with five well-developed digits. They named the 110-million-year-old fossil Tetrapodophis, which means four-legged snake. Their phylogenetic analysis placed it at the very base of the snake lineage. The scientists also identified burrowing adaptations that arguably would support an origin of snakes from fossorial rather than aquatic ancestors. Of course, the discovery was much celebrated in news reports as “a snake version of Archaeopteryx” (e.g., University of Portsmouth 2015, Christakou 2015a, Evans 2015, Yong 2015)
Yong (2015) commented in National Geographic:
Their analysis produced a family tree in which Tetrapodophis came after the earliest known snakes like Eophis, Parviraptor, and Diablophis, but is still very much a snake. But how could that be? Eophis and the others only have two legs, so how could four-legged Tetrapodophis have come after them? The answer is that evolution doesn’t proceed along simple, straight lines.
This is typical Darwinist doublespeak for the simple fact that the fossil does not fit within a Darwinian scenario without ad hoc hypotheses to explain away conflicting data. But in this case there is another little problem: all known fossils of the Jurassic earliest stem snakes (Portugalophis, Eophis, Parviraptor, and Diablophis) do not even have the body region preserved, which would show if they possessed limbs or not (see Caldwell et al. 2015), so that the above statement is also incorrect. Never believe Darwinist pop science journalists, who are notoriously sloppy with facts. But apart from this glitch, the real blows against Tetrapodophis were yet to come.
A First Blow
The first blow came with a very heated discussion about the legal status of the fossil (Christakou 2015b), even though there was no proof that any laws were broken with the export and sale of the fossil. I personally consider this discussion as very much ridiculous, given the fact that countless fossils from the quarries in Brazil were grinded for cement production or used for pavements, without any local scientist caring for this natural heritage. Now, museums around the world, which invested a lot of money and preparation effort to preserve these fossils for science, are now asked to repatriate the collections to Brazilian museums with a very poor track record of proper conservation and curation, all in the name of protecting alleged national treasures of poor countries from evil Western exploitation. Unfortunately, the pervasive woke agenda has taken hold of paleontology as well, which impairs scientific progress and has made fossil collecting to a very frustrating endeavour.
A Second Blow
The second blow came with another silly dispute about the deposition of the specimen. The specimen was deposited in a public museum in Germany as a loan by a private collector, who temporarily limited access to the specimen because it was damaged during the examination with synchrotron micro-CT scanning. Even though access was later restated and the specimen was also meticulously documented with drawings and photographs in the original publication, some scientists made absurd statements like “if the fossil can’t be studied, it doesn’t exist … I don’t want to mention the name Tetrapodophis ever again” (Gauthier quoted in Gramling 2016). Other researchers said the “original paper should not have been published, because the fossil was not officially deposited in a museum or other repository”. This reflects a common politically correct sentiment among scientists against private collections, even though many private fossil collections are better curated and more easily accessible to scientists than public collections in certain dubious countries with a reputation of sloppiness and corruption. Nevertheless, these bigoted scientists rather would leave sensational finds of high scientific value undescribed forever, than having scientific publications based on material in private collections. I find this bizarre, scientifically reprehensible, and politically highly problematic (anti private property in favor of statist bureaucracy). After all, using the same kind of reasoning we could purge all paleontological knowledge from science that is based on museum specimens that were destroyed during World War II, or lost by the post when they were sent on loan to foreign scientists, or simply cannot be relocated in the museum archives anymore, which happens way more often than many people may think. Many scientists seem to have lost their common sense nowadays.
Last but Not Least
The third and truly fatal blow came with several studies by paleontologist Michael Caldwell and his colleagues, who strongly disputed the fossorial adaptation of Tetrapodophis in favor of an aquatic adaptation, and also disputed the snake-affinity in favor of a determination as dolichosaurid lizard (Lee et al. 2016, Caldwell et al. 2016, 2021, Paparella et al. 2018), which is an extinct group of marine reptiles. The press immediately reported that the big splash was a case of mistaken identity (Geggel 2016), and that the assumed missing link between lizards and snakes has been debunked (Hodžić_2021, Lyle 2021, Strauss 2022).
One might think that this misidentification is a minor issue because dolichosaurids are often considered as close relatives of snakes within a clade Pythonomorpha. However, this opens a whole new can of worms, as the status of Pythonomorpha is subject of considerable scientific controversy itself. The Wikipedia article on Pythonomorpha has a good summary of this mess, of which the long story short is as follows: Pythonomorpha was proposed by the famous 19th century paleontologist Edward Drinker Cope (1869) to include mosasaurs and snakes as assumed close relatives, while snakes were believed to have evolved from burrowing lizards. This was rejected by most 20th century experts, who instead suggested that the closest relatives of mosasaurs are monitor lizards (e.g., Russell 1967). Then, Pythonomorpha was resurrected by Michael Caldwell and Michael Lee in the late 1990s (Caldwell & Lee 1997, Lee 1997, 1998, Caldwell 1999, Lee & Caldwell 2000) to include the aquatic extinct reptile groups aigialosaurs, mosasaurs, dolichosaurs, coniasaurs, as well as snakes, which were postulated as derived from aquatic ancestors (also see Pierce & Caldwell 2004, Palci & Caldwell 2007, Caldwell 2008, Paparella et al. 2018). This was again questioned by anatomical evidence (Zaher & Rieppel 1999) and more recent phylogenetic studies, which again placed mosasaurs with monitor lizards and snakes with skinks (Conrad 2008) or with anguinids and iguanas (Simões et al. 2020), or placed mosasaurs more basal than monitor lizards and snakes (Gauthier et al. 2012). On the other hand, more recent analyses (Palci et al. 2013a, Palci 2014, Martill et al. 2015, Reeder et al. 2015) recovered snakes and mosasaurs as sister groups and thus supported a monophyly of Pythonomorpha. The latter would also be congruent with the growing for a monophyletic group called Toxicofera, which would include all squamates with poison glands such as iguanas, monitor lizards, gila monsters, and snakes, under exclusion of skinks, gekkos, and true lizards. However, as always in phylogenetics there is also strong conflicting evidence presented by opponents of the Toxicofera hypothesis (Hargreaves et al. 2015, Mongiardino Koch & Gauthier 2018, Joffroy 2022). If we would draw a least common denominator of all published trees of the past decades, the result would be an unresolved polytomy (as I described in a recent Fossil Friday article about arachnid phylogeny), which rather agrees with the expectations of creationists than those of evolutionary biologists.
A New Turn of Events
Considering this uncertainty it is hardly a surprise that this year a new study brought a new turn of events and again confirmed the status of Tetrapodophis as most basal snake (Zaher et al. 2023). The authors remarked that “Our scorings of Tetrapodophis were based on first-hand observations of the original specimen, and our interpretations of the anatomy and attendant scoring disagree significantly with those of Caldwell et al. (2021), as do our phylogenetic results.” It does not take too much of a prophetic gift to predict that we will not have to wait very long for a rebuttal by Caldwell and his team.
Whoever may ultimately win this dispute, there is no doubt that the true reason for all this uncertainty is the simple fact that the pattern of similarities between different animal groups does not fall into a neatly ordered set of nested hierarchies as often pretended by hardcore Darwinists. In reality, incongruent patterns are all over the place. A snake-like body plan is a good example: Among tetrapod vertebrates a snake-like body only originated in caecilians (Gymnophiona) among lissamphibians and in squamates among amniotes. However, within amniotes this body plan originated not less than 26 times independently (Brandley et al. 2008, Evans 2015). Tetrapodophis could be a missing link to at least two of them respectively, or just might be number 27, who knows. What is also interesting is that scientists found “statistically significant support for at least six examples of the re-evolution of lost digits in the forelimb and hind limb” ((Brandley et al. 2008), which shows the level of absurdity that is readily accepted only to preserve the evolutionary paradigm.
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