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Tuesday 20 September 2022

By its fruit the tree is known.

 The ongoing war in Europe represents yet another failure by Christendom to live up to her claims of being Christian. It's not simply the fact that she has once again provided ammunition to the haters of Christ and his God by indulging in yet another industrial scale bloodbath. But that the leaders of the churches, rather than exerting any moderating influence, have been pouring fuel on the flames. By way of a reminder here is the kind of fruit that our Lord indicated ought to be expected of any tree planted by his God and Father John14:35KJV"By this shall all men know that ye are my disciples, if ye have love one to another" in other words the opposite of what has historically been(and indeed presently is)  the case with Christendom. Now, for the sincere truth seeker, there is a global community of Christian who have by JEHOVAH'S grace have been able to resist relentless pressure from the world's political establishment to take sides nationalistic and revolutionary wars of the present age and thus fulfill our Lord's prophecy to the glory of his God and Father .

I don't expect that my words will meet with universal agreement, indeed our Lord warn us that as was the case with him ,few will see the obvious blessing of the Lord JEHOVAH upon his people. 

John15:20NIV"Remember what I told you: ‘A servant is not greater than his master.’ If they persecuted me, they will persecute you also. If they obeyed my teaching, they will obey yours also.'" but hopefully you would at least understand why I don't find the claim that Satan could succeed in teaching his servants to live in peace while God has consistently failed to do so impressive.

Darwinists continue to not see the forest for the trees.

 Gene Sharing Is More Widespread than Thought, with Implications for Darwinism 

David Coppedge. 

Evidence is growing that organisms share existing genetic information horizontally, not just vertically. This has immense implications for neo-Darwinian theory that are not yet fully recognized. If traits can be shared across species, genera and even phyla, they are not being inherited from common ancestors. The findings might also cast stories about convergence and co-evolution in a completely different light. Let’s look at some of the news on this front. 

Introgression 

Last month, Current Biology posted a Primer on Introgression by four authors. Introgression refers to “lasting transfer of DNA from one of the species into the genome of the other” by means of hybridization and backcrossing. Basically, it describes “the incorporation of the DNA from one species into another.” 

Over the last few decades, advances in genomics have transformed our understanding of the frequency of gene flow between species and with it our ideas about reproductive isolation in nature. These advances have uncovered a rich and often complicated history of genetic exchange between species — demonstrating that such genetic introgression is an important evolutionary process widespread across the tree of life 

Figure 1 in this open-access paper shows nine photos of creatures where “gene flow” has been inferred. They include vastly different organisms, from bacteria to birds, fish, and mammals — including humans. The authors strive to maintain Darwinism in their explanation, but this realization undermines what previously was explained by convergence or by independent origins of traits: 

Instead of waiting for a beneficial mutation to arise, gene flow can instead introduce variation that has been ‘pre-tested’ by selection, allowing species to evolve rapidly. For instance, alleles causing brown winter coat color in snowshoe hares (Figure 1E), early flowering time in sunflowers or serpentine soil tolerance in Arabidopsis have introgressed from closely related species, which has facilitated adaptation to new environments. 

The authors do not speculate at this time how common adaptive introgression might be.  

Kleptomania 

In news from the Florida Museum of Natural History, biologists discussed how a new genome for ferns reveals “a history of DNA hoarding and kleptomania.” The article is classified under “Evolution” but what is Darwinian about it? 


The “hoarding” part refers to ferns having 720 pairs of chromosomes “crammed into each of its nuclei” for unknown evolutionary reasons. Whole-gene duplication is not uncommon in plants and animals, but most species slim down their genomes over time. Why has this not happened in ferns? Geneticists are still trying “to figure out the evolutionary process underlying this paradox,” the article says. 


The “kleptomania” claim refers to “the surprise discovery that ferns stole the genes for several of their anti-herbivory toxins from bacteria.” 

Rather than evolving this toxin on its own, Ceratopteris appears to have obtained it directly from bacteriathrough a process called horizontal gene transfer. And given that there were multiple copies of the gene spread out among three separate chromosomes, it’s likely this happened more than once. 

The article references a 2014 study that showed another instance of kleptomania. Ferns seem to have inherited genes for thriving in shade from distantly related plants, but “exactly how organisms separated by millions of years of evolution are able to swap fully functional genes remains unclear.”  

“The mechanisms behind horizontal gene transfer remain one of the least investigated areas of land plant evolution,” Doug Soltis explained. “Over evolutionary timescales, it’s a bit like winning the lottery. Any time a plant is wounded, its interior is susceptible to invasion from microbes, but for their DNA to be incorporated into the genome seems amazing.” 

These examples illustrate a sea change in thinking about horizontal gene transfer (HGT), which was formerly thought to be restricted to microbes. 

Library Books 

A related preprint by Haimlich et al. on bioRxiv investigated “Widespread horizontal gene transfer between plants and their microbiota.” Finding 180 genes that indicated “prevalent horizontal gene transfer,” they concluded, 

Our results suggest that horizontal gene transfer between hosts and their microbiota is a significant and active evolutionary mechanism that contributed new traits to plants and their commensal microbiota. 

Crediting evolution seems stretched, though. Information shared is not the same as information innovated, nor is borrowing a book as difficult as writing one. 


Another preprint on bioRxiv reported introgression between “highly divergent sea squirt genomes” that were brought into contact by humans. The paper suggests that hybridization of these “incompletely isolated” species offered “an adaptive breakthrough” for the organisms. What other cases of assumed allopatric speciation convergence might turn out to be cases of introgression or HGT? Can life share library books of genes across distant species? 

From Division of Labor to Expertise Sharing 

Speaking of bacteria, Duke University proclaims that “Microbial Communities Stay Healthy by Swapping Knowledge.” How and why microbes do this prompted a metaphor that portrays intelligent action: 

Put another way, a construction crew could be extremely resilient to electricians quitting if the plumbers on site also knew how to wire a building. But the same crew would be even more resilient if the remaining electricians could simply transfer their expertise to anyone on the job when needed, no matter their profession. 

Dr. Lingchong You at Duke considers HGT a “dynamic division of labor” by which bacteria maintain their health in nature. 

Human Sharing 

With these reassessments of heredity in mind, how much of assumed “human evolution” could be explained by gene sharing instead of by the neo-Darwinian mutation-selection model? Have human beings been sharing library books or downloading each other’s software apps instead of writing them from scratch?


News from the University of Tübingen says that paleoanthropologists are considering the degree to which genetic hybridization affected the human skeleton and skull shape. 

Many people living today have a small component of Neanderthal DNA in their genes, suggesting an important role for admixture with archaic human lineages in the evolution of our species. Paleogenetic evidence indicates that hybridization with Neanderthals and other ancient groups occurred multiple times, with our species‘ history resembling more a network or braided stream than a tree. Clearly the origin of humankind was more complex than previously thought. 

It’s not the percentage of Neanderthal DNA that affects the phenotype, the researchers are finding, but “the presence of particular genetic variants” instead. 


Similar conclusions are being reached at North Carolina State University where a news item says that “Ancient DNA caused a revolution in how we think about human evolution.” Out is the old single-file march of progress from ape to man. In is the “a series of streams that converge and diverge at multiple points.” The “exploratory study” going on at NC State is changing the view that evolution is driven by external environmental factors, such as climate, and toward the view that internal gene flow causes the variations in human anatomy. 

Gene Flow Everywhere 

The Tübingen story notes that evolutionary innovation by hybridization is being found everywhere:  

In other organisms — from plants to large mammals — hybridization is known to produce evolutionary innovation, including outcomes that are both novel and diverse. “It is estimated that about 10 percent of animal species produce hybrids, including, for example, bovids, bears, cats and canids,” Ackermann says. Hybrids are also known in primates, our close relatives, such as baboons, she says. “Because hybridization introduces new variation, and creates new combinations of variation, this can facilitate particularly rapid evolution, especially when facing new or changing environmental conditions.” 

A question arises whether these variations and combinations of variations are random when introduced by gene flow instead of mutation. If the latter, then old-school Darwinians might argue that they are merely additional manifestations of neo-Darwinism’s unguided process of random variation and selection. 


But if these shared genes are instead modular pieces of functional information that are pre-adapted to join up in certain ways, then biologists will need to consider whether the source of that information requires an intelligent cause. The case for intelligent design in instances of gene flow can be further strengthened by observing whether newly incorporated genes are epigenetically regulated, targeted to functional loci, and responsive to signals from the environment. If so, organisms have been equipped with mechanisms to ensure robustness to changing conditions. That implies Foresight.





Yet more on why we make a big deal about the Name.

 Exodus 14:4ASV"4And I will harden Pharaoh's heart, and he shall follow after them; and I will get me honor upon Pharaoh, and upon all his host: and the Egyptians shall know that I am Jehovah. And they did so."

11For from the rising of the sun even unto the going down of the same my name'shall be great among the Gentiles; and in every place incense'shall be offered unto my name, and a pure offering: for my name'shall be great among the Gentiles, saith Jehovah of hosts. 

 The Lord JEHOVAH is determined to have his name exalted above the names of the false gods ,as his loyalists we are simply responding to the current of his Spirit. The great enemy of God and his loyalists is ,of course ,bent on the erasure of the divine name, ,doubtless as retaliation for the erasure of his own name. The title 'Satan' (meaning enemy)by which he is referred to in scripture is not a self designation but the sentence pronounced upon him by the Lord JEHOVAH. So it's no surprise that in the present civilisation,of which Satan is architect and ruler, there is widespread Animus toward the divine name. For instance I have never seen a bible translation with the names of false gods like Zeus and Marduk substituted by titles, but the same translators have no problem disrespectfully removing JEHOVAH'S name from his own book.

So then whose will are they fulfilling? That loyal servant of JEHOVAH who declared :John17:26KJV"26And I have declared unto them thy name, and will declare it: that the love wherewith thou hast loved me may be in them, and I in them." 

Or the the enemy of the Lord JEHOVAH and his loyalists.

And yet even more on why the OOL Remains the keystone of the design argument.

 All Living Systems Must Process Energy, Store and Utilize Information, and Replicate 

Walter Bradley

Casey Luskin 

Editor’s note: We are delighted to present a series by Walter Bradley and Casey Luskin on the question, “Did Life First Arise by Purely Natural Means?” This is the second entry in the series, a modified excerpt from the recent book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. Find the full series so far here.  

Aristotle posited the idea of spontaneous generation of life from nonliving matter, or abiogenesis, that held sway for two millennia. But in 1859, Louis Pasteur showed persuasively — with a clever set of experiments — that what appeared to be life springing forth from nonliving matter was actually life emerging from exceedingly small living organisms, not lifeless matter. Pasteur’s experiments were widely seen as having settled the question of whether life could only come from preexisting living matter, a process called biogenesis. In 1864, Pasteur triumphantly predicted to the science faculty at the Sorbonne in Paris, “Never will the doctrine of spontaneous generation recover from the mortal blow of this simple experiment.”1 Pasteur’s view remained dominant for almost a century. 


In 1924, after sixty years of virtual silence since Pasteur’s experiments, the Russian biochemist Alexander Ivanovich Oparin proposed that the complex molecular arrangements and associated functions of living systems evolved from simpler molecules that preexisted on the lifeless, primitive Earth. With this bold speculation, a recognizably modern hypothesis of how life might have arisen, Oparin reopened the discussion of abiogenesis.2 

A Rationalist Biologist 

In 1929, the British biologist J. B. S. Haldane published a paper in the Rationalist Annual speculating on what initial conditions might be most favorable for a naturalistic origin of life.3 He imagined an early Earth atmosphere rich in gases that was acted upon by lightning that caused chemical reactions to produce various building blocks for life — such as sugars and simple amino acids. In Haldane’s view, these molecules might become sufficiently concentrated in oceans, or more likely in lakes and ponds, such that they could chemically react to form long polymer chains that today we know are the key components in living cells (i.e., protein, DNA, and RNA).4 In 1944, the noted quantum physicist Erwin Schrödinger observed that living systems are characterized by highly ordered, aperiodic structures that survive by continually utilizing (chemical or radiant) energy from their surroundings.5 In 1952, Harold C. Urey proposed that the Earth’s early atmosphere was rich in hydrogen, ammonia, and methane—chemicals that both provided the elemental building blocks and the energy to facilitate the chemical reactions necessary to make primary biopolymers, the chemical building blocks of life.6 

Many Additional Steps 

The review above outlines early theories about generating the building blocks of life on Earth. But many additional steps would be needed for the origin of life to occur, which are sketched in the figure below.7 In our next post in this series, these various steps in a hypothetical origin-of-life scenario will be reviewed so that you can judge for yourself whether current theories are plausible. 


 

Figure: Major steps involved in the origin of life. All prebiotic evolutionary scenarios contain many hypothetical steps. Credit: Casey Luskin, modified with permission after Committee for Integrity in Science Education, Teaching Science in a Climate of Controversy: A View from the American Scientific Affiliation (Ipswich, MA: American Scientific Affiliation, 1986), 31.  

 First, though, it is vital to define the problem. As noted already, all living systems (1) process energy, (2) store information, and (3) replicate. In nature, these processes are performed primarily by molecules from three families of large biopolymers: proteins, DNA, and RNA. The mystery of how life began is essentially the mystery of how these three types of biopolymers formed and congregated within a cell with a barrier made of lipids as a self-replicating system. 

Notes 

1)R. L. Devonshire, The Life of Pasteur, translated R. Vallery-Radot (New York: Doubleday, 1920), 109.

2)Alexander I. Oparin, Proiskhozhdenie Zhizni (Moscow, Russia: Izd. Moskovski Rabochii, 1924), translated as Origin of Life by S. Morgulis (New York: Macmillan, 1938).

3)J. B. S. Haldane, “Origin of Life,” Rationalist Annual 148 (1929), 3-10. For a discussion of Haldane’s views, see Stéphane Tirard, “J.B.S. Haldane and the origin of life,” Journal of Genetics 96 (November 2017), 735-739.

4)Y. D. Bernal, “The Physical Basis of Life,” paper presented before British Physical Society in 1949, found in The Physical Basis of Life (London, UK: Routledge, 1951).

5)Erwin Schrödinger, What Is Life? The Physical Aspect of the Living Cell (Cambridge, UK: Cambridge University Press, 1944).

6)Harold C. Urey, The Planets: Their Origin and Development (New Haven, CT: Yale University Press, 1952).

And yet more on why the OOL remains the keystone of the design argument.

Did Life First Arise by Purely Natural Means? 

Walter Bradley

Casey Luskin 

Editor’s note: We are delighted to present a series by Walter Bradley and Casey Luskin on the question, “Did Life First Arise by Purely Natural Means?” This is the first entry in the series, a modified excerpt from the recent book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. Find the full series so far here.

Major scientific magazines and journals often feature articles on the “Biggest Unsolved Mysteries in Science”1 — and the origin of life is almost always on that list, sometimes as the number one mystery.2 In this and coming posts we will explore key challenges to a natural, chemical origin of life. We’ll examine the formation of the essential functional polymers of life — proteins, DNA (deoxyribonucleic acid), and RNA (ribonucleic acid). How might these extraordinarily complex molecules have formed in oceans, lakes, or ponds from simple, naturally occurring molecular building blocks like sugars and amino acids? What is life? How does it operate? Could life originate by strictly natural means? 

Three Scientific Discoveries 

Darwin’s theory of evolution and the development of the second law of thermodynamics by Boltzmann and Gibbs are two of the three major scientific discoveries of the 19th century. Maxwell’s field equations for electricity and magnetism are the third. The second law of thermodynamics has had a unifying effect in the physical sciences much like the theory of evolution has had in the life sciences. What is intriguing is that the predictions of one seem to contradict the predictions of the other. The grand story of evolution teaches that living systems have generally moved from simpler to more complex over time.3 The second law of thermodynamics teaches just the opposite, a progression from order to disorder, from complexity to simplicity in the physical universe. Your garden and your house, left to themselves, go from order to disorder. But you can restore the order if you do the necessary work. In the winter, when it is cold, the interior of your house will gradually drop in temperature toward the outside temperature. But a gas heater can reverse this process by converting the chemical energy in natural gas into thermal energy in the house.  

True Everywhere in Life 

This simple analogy illustrates what is true of all living systems: they can only live by having access to energy and a means of converting this energy into the alternative forms of energy or work required to oppose the pull toward thermodynamic equilibrium, from complexity to simplicity. Living systems are much more complex than nonliving systems. Like a lawnmower with gasoline as a source of energy and an engine to convert that energy into movement of a blade to cut the grass, living systems must have access to sources of energy and systems to convert the energy into the needs of plants and animals. Nonliving objects in nature exist without any complex functional systems or any energy flow requirements. They are generally made of simple crystalline or amorphous materials. A picture of my (Walter Bradley’s) backyard (at the top of this article) shows a region in the foreground that is completely shaded by a large oak tree; it receives no sunlight, and consequently, has no grass. Adjacent to this shadowy, bare section is a region where sunlight is present about 50 percent of the daytime and consequently has a beautiful, grassy cover. The second law of thermodynamics is a law of nature (like gravity, everyone is subject to it). Living plants and animals can survive only with energy flowing through their systems. Nonliving objects such as mountains, rocks, sand, rivers, and soil have no need for energy flow, nor do they have the complexity to utilize energy toward some goal.  


To Utilize and Store Energy 

To summarize, plants can utilize solar energy to levitate above thermodynamic equilibrium. Nonliving objects such as mountains, oceans, rocks, sand, and soil have no need for such complexity; they do not store chemical energy like plants do; nor can they process solar or other forms of energy. Living matter is much more complex (e.g., RNA, DNA, protein, etc.), needing as it does to be able to utilize and store available energy from the sun or from the consumption of plants and animals.  

Notes 

1)See for example Ronak Gupta, “The 7 biggest unsolved mysteries in science,” Digit (May 26, 2015), https://www.digit.in/features/general/7-greatest-unsolved-problems-in-science-26132.html (accessed November 18, 2020).

2)See for example Philip Ball, “10 Unsolved Mysteries in Chemistry,” Scientific American (October 2011), https://www.scientificamerican.com/article/10-unsolved-mysteries/ (accessed November 18, 2020).

3)Technically the official line from neo-Darwinian evolutionists is that evolution knows nothing of “progress” and does not necessarily move from “simple to more complex.” Nonetheless, it is also true that the grand arc of the evolutionary story moves from simpler organisms toward more complex ones. In this evolutionary story, biological and organic systems began with a single self-replicating molecule and ended up at us. Evolutionary theorists sometimes try to trivialize this clear progression by calling it “bouncing off the lower wall of complexity,” but it cannot be denied that their story entails a march towards greater complexity. See for example Stephen Jay Gould, Full House: The Spread of Excellence from Plato to Darwin (New York: Three Rivers, 1996).