Druzism: a brief history.

Druze are members of an Arabic-speaking esoteric ethnoreligious group originating in Western Asia. They practice Druzism, an Abrahamic, monotheistic, syncretic, and ethnic religion based on the teachings of Hamza ibn Ali ibn Ahmad and the sixth Fatimid caliph, al-Hakim bi-Amr Allah, and Ancient Greek philosophers such as Plato, Aristotle, Pythagoras, and Zeno of Citium. Adherents of the Druze religion are called The People of Monotheism (Al-Muwaḥḥidūn).

The Epistles of Wisdom is the foundational and central text of the Druze faith. The Druze faith incorporates elements of Isma'ilism, Gnosticism, Christianity, Zoroastrianism, Buddhism, Hinduism, Neoplatonism, Pythagoreanism, and other philosophies and beliefs, creating a distinct and secretive theology based on an esoteric interpretation of scripture, which emphasizes the role of the mind and truthfulness. Druze believe in theophany and reincarnation. Druze believe that at the end of the cycle of rebirth, which is achieved through successive reincarnations, the soul is united with the Cosmic Mind (al-ʻaql al-kullī).

Even though the faith originally developed out of Isma'ilism, Druze do not identify as Muslims. The Druze faith is one of the major religious groups in the Levant, with between 800,000 and a million adherents. They are found primarily in Lebanon, Syria, and Israel, with small communities in Jordan. They make up 5.5% of the population of Lebanon, 3% of Syria and 1.6% of Israel. The oldest and most densely-populated Druze communities exist in Mount Lebanon and in the south of Syria around Jabal al-Druze (literally the "Mountain of the Druze").

The Druze community played a critically important role in shaping the history of the Levant, where it continues to play a significant political role. As a religious minority in every country in which they are found, they have frequently experienced persecution by different Muslim regimes, including contemporary Islamic extremism. 

Stephen Hawking: a brief history.

Stephen William Hawking CH CBE FRS FRSA (8 January 1942 – 14 March 2018) was an English theoretical physicist, cosmologist, and author who was director of research at the Centre for Theoretical Cosmology at the University of Cambridge at the time of his death. He was the Lucasian Professor of Mathematics at the University of Cambridge between 1979 and 2009.

Hawking was born in Oxford into a family of doctors. He began his university education at University College, Oxford, in October 1959 at the age of 17, where he received a first-class BA degree in physics. He began his graduate work at Trinity Hall, Cambridge, in October 1962, where he obtained his PhD degree in applied mathematics and theoretical physics, specialising in general relativity and cosmology in March 1966. In 1963, Hawking was diagnosed with an early-onset slow-progressing form of motor neurone disease that gradually paralysed him over the decades. After the loss of his speech, he communicated through a speech-generating device initially through use of a handheld switch, and eventually by using a single cheek muscle.

Hawking's scientific works included a collaboration with Roger Penrose on gravitational singularity theorems in the framework of general relativity and the theoretical prediction that black holes emit radiation, often called Hawking radiation. Initially, Hawking radiation was controversial. By the late 1970s and following the publication of further research, the discovery was widely accepted as a significant breakthrough in theoretical physics. Hawking was the first to set out a theory of cosmology explained by a union of the general theory of relativity and quantum mechanics. He was a vigorous supporter of the many-worlds interpretation of quantum mechanics.

Hawking achieved commercial success with several works of popular science in which he discussed his theories and cosmology in general. His book A Brief History of Time appeared on the Sunday Times bestseller list for a record-breaking 237 weeks. Hawking was a Fellow of the Royal Society, a lifetime member of the Pontifical Academy of Sciences, and a recipient of the Presidential Medal of Freedom, the highest civilian award in the United States. In 2002, Hawking was ranked number 25 in the BBC's poll of the 100 Greatest Britons. He died on 14 March 2018 at the age of 76, after living with motor neurone disease for more than 50 years. 

The Big bang: a brief history.

 The Big Bang theory is the prevailing cosmological model explaining the existence of the observable universe from the earliest known periods through its subsequent large-scale evolution. The model describes how the universe expanded from an initial state of high density and temperature, and offers a comprehensive explanation for a broad range of observed phenomena, including the abundance of light elements, the cosmic microwave background (CMB) radiation, and large-scale structure.

Crucially, the theory is compatible with Hubble–Lemaître law—the observation that the farther away a galaxy is, the faster it is moving away from Earth. Extrapolating this cosmic expansion backwards in time using the known laws of physics, the theory describes an increasingly concentrated cosmos preceded by a singularity in which space and time lose meaning (typically named "the Big Bang singularity"). Detailed measurements of the expansion rate of the universe place the Big Bang singularity at around 13.8 billion years ago, which is thus considered the age of the universe.

After its initial expansion, an event that is by itself often called "the Big Bang", the universe cooled sufficiently to allow the formation of subatomic particles, and later atoms. Giant clouds of these primordial elements—mostly hydrogen, with some helium and lithium—later coalesced through gravity, forming early stars and galaxies, the descendants of which are visible today. Besides these primordial building materials, astronomers observe the gravitational effects of an unknown dark matter surrounding galaxies. Most of the gravitational potential in the universe seems to be in this form, and the Big Bang theory and various observations indicate that this excess gravitational potential is not created by baryonic matter, such as normal atoms. Measurements of the redshifts of supernovae indicate that the expansion of the universe is accelerating, an observation attributed to dark energy's existence.

Georges Lemaître first noted in 1927 that an expanding universe could be traced back in time to an originating single point, which he called the "primeval atom". Edwin Hubble confirmed through analysis of galactic redshifts in 1929 that galaxies are indeed drifting apart; this is important observational evidence for an expanding universe. For several decades, the scientific community was divided between supporters of the Big Bang and the rival steady-state model which both offered explanations for the observed expansion, but the steady-state model stipulated an eternal universe in contrast to the Big Bang's finite age. In 1964, the CMB was discovered, which convinced many cosmologists that the steady-state theory was falsified, since, unlike the steady-state theory, the hot Big Bang predicted a uniform background radiation throughout the universe caused by the high temperatures and densities in the distant past. A wide range of empirical evidence strongly favors the Big Bang, which is now essentially universally accepted.

Primeval tech continues to deconstruct Darwininism.

 

Tricks of the Cell Trade

Evolution News @DiscoveryCSC

Both cables on a suspension bridge snap. It’s going to collapse. If repairmen cannot mend the cables extremely rapidly, the bridge is doomed, and all the cars on it will dump into the water. Time is of the essence. The task looks hopeless. What to do?

Homologous Recombination

Cells face that kind of challenge every day, but they are well equipped to handle it. When both DNA strands break (the “double-stranded break” crisis, or DSB), a cell can die. Molecular machines fly into action as the strands flail about, threatening genomic catastrophe. The repair crew has an additional problem: unlike the bridge cable, the DNA strand is made up of a sequence of code that needs to match what was there before the DSB. In a process called homologous recombination, the machinery searches for a template to rebuild the broken sequence. Researchers at Uppsala University know that this process is mostly “well described in the literature.”

However, the description usually disregards the daunting task of finding the matching template among all the other genome sequences. The chromosome is a complex structure with several million base pairs of genetic code and it is quite clear that simple diffusion in 3D would not be sufficiently fast by a long shot. But then, how is it done? This has been the mystery of homologous recombination for 50 years. From previous studies, it is clear that the molecule RecA is involved and important in the search process, but, up until now, this has been the limit of our understanding of this process. [Emphasis added.]

Even a simple bacterium knows a trick to make the search easier. It reduces the search from a 3D problem to a 2D problem. With that shortcut, the cell reduces the time to repair down to 15 minutes on average. The Uppsala group, using CRISPR and fluorescent tags, watched the RecA proteins in real time. They published their findings in Nature.

“We can see the formation of a thin, flexible structure that protrudes from the break site just after the DNA damage. Since the DNA ends are incorporated into this fiber, it is sufficient that any part of the filament findsthe precious template and thus the search is theoretically reduced from three to two dimensions. Our model suggests that this is the key to fast and successful homology repair,” says Arvid Gynnå, who has worked on the project throughout his PhD studies.

Earth’s Electrical Grid

The world beneath our feet is electrically wired. That’s the surprising announcement from Yale University about bacteria that live in soil and under the seafloor. 

A hair-like protein hidden inside bacteria serves as a sort of on-off switch for nature’s “electric grid,” a global web of bacteria-generated nanowires that permeates all oxygen-less soil and deep ocean beds, Yale researchers report in the journal Nature.

“The ground beneath our feet, the entire globe, is electrically wired,” said Nikhil Malvankar, assistant professor of molecular biophysics and biochemistry at the Microbial Science Institute at Yale’s West Campus and senior author of the paper. “These previously hidden bacterial hairs are the molecular switch controlling the release of nanowires that make up nature’s electrical grid.”

The Yale team found more about the “pili” which were thought to be made of a surface proteins by that name. Their findings, also published in Nature, we learn, call into question “thousands of publications about pili.” Pili are not the nanowires; they are machines that pump the nanowires out of the cell. Bacteria use these electrical conduits for respiration. Lacking access to oxygen (the primary electron receptor of oxygen-breathing organisms like humans), the bacteria use nanowires like snorkels to “breathe minerals” below the surface. The nanowires push excess electrons up and out of sediments.

A short animation shows how the pili work. They extend and retract repeatedly, pushing the nanowires out a bit at a time. Engineers might watch this trick to solve the problem of how to push a rope! The nanowires from bacteria link up and can extend a considerable distance on a bacterial scale. Because they conduct electrons, are ubiquitous around the earth, and provide global recycling services (see here), the nanowires justify the description of “nature’s electrical grid” under our feet. For fun, consider a new kind of silicon-impregnated wood flooring that generates electricity. Just walking on the floor, invented in Switzerland, can generate enough electricity to power a light bulb, reports Science Daily.

Tunnel Experts

A robot spacecraft, resembling an old Apollo lunar lander, touches down secretly on an enemy cargo ship. Underneath, a powerful drill breaks through the steel exterior. Material flows into the breach, melting the metal casing and building a tunnel through which the craft sends code to infect the enemy ship’s computers. Moments later, the enemy ship explodes, releasing hundreds of copies of the robot to go fight other enemy ships.

Viruses do things like that. A good one, the T7 bacteriophage, protects us from E. coli infections. Scientists in Spain, publishing in PNAS, learned more about how T7 builds its export tunnel through which it sends DNA into the harmful bacterial cell. 

Bacteriophage T7 infects Escherichia coli bacteria, and its genomic DNA traverses the bacterial cell envelope,but the precise mechanism used by the virus remains unknown. Previous studies suggested that proteins found inside the viral capsid (core proteins) disassemble and reassemble in the bacterial periplasm to form a DNA translocation channel. In this article, we have solved the structure of two different assemblies of the core proteins gp15 and gp16. These findings confirm the ability of core proteins to form tubes compatible with the periplasmic space and show the location of the transglycosylase enzyme involved in peptidoglycan degradation. Our results reveal key structural details of the assembly of the core translocation complex involved in the DNA transport through the bacterial wall.

The paper mentions an interesting fact: “Bacteriophages (phages) are viruses that infect bacteria and are considered to be the most abundant entities on Earth.” 

Windows on the Unseen

In each of these discoveries, cryo-electron microscopy opened windows to unseen realities. This revolutionary tool and other methods of super-resolution microscopy are enabling scientists to see biological wonders that have existed as far back as the first bacterial cells, but have been hidden from our eyes till now. Step by step, molecule by molecule, the evidence for intelligent design at the tiniest levels of life is coming into focus. With more academicians taking leave of Darwin, how can the scientific community deny a seat at the table to design proponents who have the necessary and sufficient causes to explain these things? 

Neil Thomas, calling the materialist paradigm a “flawed hypothesis” that is “squandering public trust,” concludes that it’s time to open the doors to alternatives:

Faced with the sheer unfeasibility of a purely natural explanation, logic leaves us with little other choice. Extending the old adage that nothing comes of nothing, it might be contended that real life, in contradistinction to the magician’s claim of a rabbit magically emerging from the hat, nothing can “magically emerge” or “naturally evolve” without a supporting agency — little though we may know of that originating agency. In default of a better explanation than that offered by the Darwinian paradigm and its various materialistic descendants and kissing cousins, however, this hypothesis surely cannot be discounted out of hand. 

NEIL THOMAS, TAKING LEAVE OF DARWIN, P. 143

More on evolution by design vs. Design by evolution.

 

The Design Connection in Biological Tracking Systems

Brian Miller

In my last article, I summarized a lecture presented at CELS (Conference on Engineering in Living Systems) that presented a model for adaptation based on the engineering principles employed in human engineered tracking systems. Now I will address the connection between these principles and the design inference.  

As a review, biological adaptation is often driven by systems that employ three subsystems:

• Sensors that monitor specific environmental conditions.
• Logic-based analyzers such as switches that trigger responses when certain conditions occur. 
• Mechanisms that drive targeted output responses.

Irreducible Complexity and Timescales 

To say that such tracking systems could not have evolved gradually almost goes without saying. Many examples of NGE do not even directly help an individual organism but only an entire population acting in concert. For instance, increasing the mutation rate to rapidly generate targeted genetic variation will often assist only a few lucky individuals to survive extreme threats such as an antibiotic.  

More generally, not only are all tracking systems irreducibly complex, but they require the subsystems to be meticulously integrated. And the integrating components, such as switches (here, here), correspond to far greater amounts of information than what could have been generated in the available timeframes. This challenge is highlighted by the fact that timescales (waiting times) grow exponentially with the amount of required new information (here, here).

The Design Connection

The presence of highly controlled adaptive mechanisms directly correlates to life employing top-down design that must meet numerous tight engineering constraints. If organisms resulted from haphazard undirected processes, their design constraints would be few and highly flexible. Altering anatomy and/or physiology should then be relatively easy, and the same undirected processes could potentially drive the changes. In contrast, the presence of numerous tight constraints correlates with altering the system being far more difficult. Significant changes would typically require highly specified and coordinated modifications. 

Szallasi et al. in Systems Modeling in Cellular Biology tacitly came to this same conclusion:

An often noted reservation against the type of analogies between biological and engineered systems we brought forward states that these two types of complex systems arise in fundamentally different ways, namely through evolution versus purpose-driven, top-down design (see, for example, Bosl and Li (2005)). Clearly, evolvability is of paramount importance for living systems (Kirschner and Gerhart, 1998). Here, we think of evolvability simply (maybe naively) in the sense of controlled and structured change in lineages, rather than cells, on long time scales in response to perhaps large variations in the environment. At the population level (of all engineered systems of one type), evidently progress in engineering fulfills similar criteria. [Emphasis added.]

P. 32

Note how the authors do not describe evolution using such traditional terms as “random” and “undirected.” Instead, they describe change as “controlled” and “structured.” Their description of evolvability sounds less like neo-Darwinian evolution than like technological innovation. 

Evolution by design vs. Design by evolution.

 

Nearly All of Evolution Is Best Explained by Engineering

Brian Miller

In recent articles, I have summarized lectures at CELS (Conference on Engineering in Living Systems) that described an engineering model for adaptation and explained how adaptation derives from organisms’ internal capacities (here, link). Now I will summarize another CELS lecture that expanded upon these themes by outlining a second complementary engineering model for adaptation. 

Comparing Models

Standard evolutionary theory assumes that genetic variation expands through DNA mutating or otherwise altering randomly. Concurrently, natural selection and other processes transform species over time gradually through numerous, successive, slight modifications. The results are unpredictable, and in different subpopulations they can vary greatly. 

In stark contrast, the presented engineering-based model assumes that organisms adapt to the environment using the same engineering principles seen in human tracking systems (here, here). More specifically, they continuously monitor the environment and track pre-specified environmental conditions. When the right conditions occur, internal mechanisms induce pre-determined responses such as targeted genetic changes, physiological adjustments, and/or anatomical alterations. These adaptive processes are directed by irreducibly complex systems that consistently include three components:

• Sensors to detect pre-specified environmental conditions such as temperature.
• Logic-based analyzers that determine if specific criteria are met such as the temperature exceeding a set point. When criteria are met, the analyzers send signals to trigger the appropriate responses. 
• Processes that generate predetermined output responses when triggered, such as growing thinner hair.

The resulting changes are targeted, rapid, and often reversible. They are also predictable and repeatable. And their magnitude can range from minor alterations to dramatic transformations, but changes are bounded and predefined. 

Over the past few decades, every facet of the engineering model has been increasingly affirmed by everyone from mainstream biologists to third-wave evolutionists to leading creationists (here, here, here, here). The strongest supportive evidence comes from studies of what have been termed natural genetic engineering (NGE) and phenotypic plasticity. 

Natural Genetic Engineering

NGE refers to genetic alterations that are not random. Instead, they result from cells employing highly complex machinery to direct targeted DNA modifications. Leading researcher James Shapiro describes the processes in a 2016 review article:

Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.

He further elaborates on the editing systems in a 2017 review article:

Like all classes of cellular biochemistry, NGE DNA transport and restructuring functions are subject to control by regulatory circuits and respond to changing conditions…NGE activities typically affect multiple characters of the variant cell and organism. Consequently, major phenotypic transformations can occur in a single evolutionary episode and are not restricted to a gradual accumulation of ‘numerous, successive, slight modifications.’

One could contest Shapiro’s claims about what NGE accomplished in the past, but his general description clearly matches the engineering model’s central features. The regulatory circuits that respond to environmental conditions correspond to sensors integrated with logic mechanisms. And the transport and restructuring functions correspond to specified output responses. In addition, the DNA modifications are targeted, rapid, and bounded as the engineering model expects.

NGE has been identified in all domains of life from the simplest to the most complex. Yeast cells respond to nutrient starvation by increasing the mutation rates at specific locations referred to as mutational hot spots. And the remarkable diversity in dog breeds is not the result of completely random mutations, but it also results from mutational hot spots that allow for increases in targeted genetic variation that can drive rapid adaptation. Biophysicists John Fondon and Harold Garner noted:

The high frequency and incremental effects of repeat length mutations provide molecular explanations for swift, yet topologically conservative morphological evolution…We hypothesize that gene-associated tandem repeats function as facilitators of evolution, providing abundant, robust variation and thus enabling extremely rapid evolution of new forms.

Equally striking, plant genomes contain DNA segments known as transposable elements (TEs) that can move to new locations, allowing them to alter the activity of local genes. Specific environmental stimuli can initiate relocation to target locations (here, here), and stimuli can activate the TEs, resulting in adaptive benefits. For instance, TEs modify gene regulation in maize to confer drought tolerance, alter flowering time, and enable plants to grow in toxic aluminum soils (here, here).

Phenotypic Plasticity

Phenotypic plasticity refers to an organism’s ability to transform its anatomy and physiology in response to environmental stimuli. The changes do not result from genetic alterations but from internal adaptive mechanisms. Developmental biologist Ralf Sommer enumerated these mechanisms’ essential components in a 2020 review article:

…plasticity requires developmental reprogramming in the form of developmental switches that can incorporate environmental information. However, the associated molecular mechanisms are complicated, involving complex loci, such as eud-1, that function as switches and GRNs. While still early, it is likely that switch genes point to a general principle of plasticity because other examples of plasticity also involve complex switch mechanisms.

The “incorporation of environmental information” tacitly implies the presence of sensors and signal transmission pathways. The switch incorporating the sensory output equates to a logic-based analyzer, and the gene regulatory network (GRN) activity corresponds to the output response. In summary, the core components perfectly match those of the engineering model for adaptation. 

Phenotypic plasticity has been observed in numerous species in diverse taxa. Gulls of the family Laridae track the sodium level in their blood with sensors in heart vessels. When the level reaches a threshold, gulls generate a specialized gland that extracts excess sodium from the blood and excretes it through the beak. If the gull migrates to a freshwater environment, the gland disappears. 

Cichlid fish demonstrate phenotypic plasticity for multiple traits. Muschick et al. in a 2011 study raised Midas cichlids on food with different hardnesses. The different diet groups developed significantly different pharyngeal jawbones, and the differences resembled qualitatively the differences in jawbones found in specialized species. Härer et al. in a 2019 study exposed Midas cichlids to light of different frequencies. In response to a change in frequency, the cichlids switched the expression of cone opsin genes crucial for color vision in only a few days. Other such mechanisms likely exist, based on the observation that cichlids rapidly converge to the same basic forms repeatedly. 

As a final example, fish residing in cave environments display distinctive traits such as reduced eyes and pigmentation. The standard evolutionary story is that these traits gradually developed through natural selection. But experiments over the past decade on the effects of exposing fish to cave-like conditions are changing the narrative. 

Rohner et al. in a 2013 study raised A. mexicanus embryos in water with low conductivity mimicking cave conditions. The embryos developed into adults with significantly smaller eyes. Corral and Aguirre in a 2019 study raised A. mexicanus in different temperatures and different levels of water turbulence. The variant conditions resulted in adult fish differing in vertebral number and body shape. For instance, fish raised in more turbulent water displayed more streamlined bodies and extended dorsal and anal fin bases that improved their mobility in that environmental condition. And Bilandžija et al. in a 2020 study raised the same species in darkness, and the fish developed many cave-related traits such as resistance to starvation and altered metabolism and hormone levels. Future research will likely uncover even more examples where cave-specific adaptations result not from random mutations but from internal mechanisms. 

Future Research

The engineering model not only best fits the latest experimental and observational data, but it can help guide future research. Whenever a species rapidly and predictably adapts to a specific environmental condition (here, here, here), investigators can expect that changes are directed by sensors, logic-based analyzers, and output response mechanisms. They can then focus research on identifying and understanding these components. 

Traditional evolutionary processes do play a part in biological adaptation, but mounting evidence demonstrates that their role is relatively minor in the drama of life (here, here). Instead, engineered adaptive mechanisms that direct targeted modifications perform on center stage.