Can this tree be re-planted?

Sara Walker and Her Crew Publish the Most Interesting Biology Paper of 2022 (So Far, Anyway)

Paul Nelson

 

 

We’ve just ended the first quarter of the year. It’s a long way to New Year’s Eve 2022. But this new open access paper from senior author Sara Walker (Arizona State) and her collaborators will be hard to top, in the “Wow, that is so interesting!” category. (The first author of this paper is Dylan Gagler, so we’ll refer to it as “Gagler et al. 2022” below.)

1. Back in the day, the best evidence for a single Tree of Life, rooted in the Last Universal Common Ancestor (LUCA), was the apparent biochemical and molecular universality of Earth life.

Leading neo-Darwinian Theodosius Dobzhansky expressed this point eloquently in his famous 1973 essay, “Nothing in biology makes sense except in the light of evolution”:

The unity of life is no less remarkable than its diversity…Not only is the DNA-RNA genetic code universal, but so is the method of translation of the sequences of the “letters” in DNA-RNA into sequences of amino acids in proteins. The same 20 amino acids compose countless different proteins in all, or at least in most, organisms. Different amino acids are coded by one to six nucleotide triplets in DNA and RNA. And the biochemical universals extend beyond the genetic code and its translation into proteins: striking uniformities prevail in the cellular metabolism of the most diverse living beings. Adenosine triphosphate, biotin, riboflavin, hemes, pyridoxin, vitamins K and B12, and folic acid implement metabolic processes everywhere. What do these biochemical or biologic universals mean? They suggest that life arose from inanimate matter only once and that all organisms, no matter now diverse, in other respects, conserve the basic features of the primordial life.[Emphasis added.]

For Dobzhansky, as for all neo-Darwinians (by definition), the apparent molecular universality of life on Earth confirmed Darwin’s prediction that all organisms “have descended from some one primordial form, into which life was first breathed” (1859, 494) — an entity now known as the Last Universal Common Ancestor, or LUCA. So strong is the pull of this apparent universality, rooted in LUCA, that any other historical geometry seems unimaginable.

The “Laws of Life”

Theoretician Sara Walker and her team of collaborators, however, are looking for an account of  what they call (in Gagler et al. 2022) the “laws of life” that would apply “to all possible biochemistries” — including organisms found elsewhere in the universe, if any exist. To that end, they wanted to know if the molecular universality explained under neo-Darwinian theory as material descent from LUCA (a) really exists, and (b) if not, what patterns do exist, and how might those be explained without presupposing a single common ancestor.

And a single common ancestor, LUCA? That’s what they didn’t find.

2. Count up the different enzyme functions — and then map that number within the total functional space.

Many thousands of different enzyme functional classes, necessary for the living state, have been described and catalogued in the Enzyme Commission Classification, according to their designated EC numbers. These designators have four digits, corresponding to progressively more specific functional classes. For instance, consider the enzyme tyrosine-tRNA ligase. Its EC number, 6.1.1.1, indicates a nested set of classes: EC 6 comprises the ligases (bond-forming enzymes); EC 6.1, those ligases forming carbon-oxygen bonds; 6.1.1, ligases forming aminoacyl-tRNA and related compounds; finally, 6.1.1.1, the specific ligases forming tyrosine tRNA. (See Figure 1.)

The Main Takeaway from This Pattern? 

Being a ligase — namely, an enzyme that forms bonds using ATP — entails belonging to a functional group, but not a group with material identity among its members. A rough parallel to a natural language such as English may be helpful. Suppose you wanted to express the idea of “darkness” or “darkened” (i.e., the relative absence of light). English supplies a wide range of synonyms for “darkened,” such as:

• murky
• shaded
• shadowed
• dimmed
• obscured

The same would be the case — the existence of a set of synonyms, i.e., words with the same general meaning, but not the same sequence identity — for any other idea. The concept of something being “blocked,” for instance, takes the synonyms:

• jammed
• occluded
• prevented
• obstructed
• hindered

While these words convey (approximately) the same meaning, and hence fall into the same semantic functional classes, they are not the same character strings. Their locations in an English dictionary, ordered by alphabet sequence, may be hundreds of pages apart. Moreover, as studied by the discipline of comparative philology, the historical roots of a word such as “hindered” will diverge radically from its functional synonyms, such as “blocked.” These two words, although semantically largely synonymous, enter English from originally divergent or unrelated antecedents — a character string gap still reflected by their very different spellings.

A strikingly similar pattern obtains with the critical (essential) components of all organisms. Gagler et al. 2022 looked at the abundances of enzyme functions across the three major domains of life (Bacteria, Archaea, Eukarya), as well as in metagenomes (environmentally sampled DNA). What they found was remarkable — a finding (see below) which may be easier for non-biological readers to understand via another analogy.

3. A segue into computer architectures — then back to enzymes.

The basic architecture of laptop computers includes components present in any such machine, defined by their functional roles:

• Central processing unit (CPU) — the primary logic operator
• Memory — storage of coded information
• Power supply — electrons (energy) needed for anything at all to be computed

And so on. (Although exploring this point in detail would take us far afield, it is worth noting that in 1936, when Alan Turing defined a universal computational machine, he did so with no idea about the arrival, decades down the road, of silicon-based integrated circuits, miniaturized transistors, motherboards, solid-state memory devices, or any of the rest of the material parts of computers now so familiar to us. Rather, his parts were functionally, not materially defined, as abstractions occupying the various roles those parts would play in the computational process — whatever their material instantiation would later turn out to be.) Now suppose we examined 100,000 laptops, randomly sampled from around the United States, to see what type of CPU — meaning which material part (e.g., built by which manufacturer) — each machine used as its primary logic operator.

A range of outcomes is possible (see Figures 2A and 2B). For instance, if we plot CPUs from different manufacturers on the y axis, against the total number of laptop parts inspected on the x axis, it might be the case that the distribution of differently manufactured (i.e., materially distinct) CPUs would scale linearly with laptops inspected (Figure 2A). In other words, as our sample of inspected laptop parts grows, the number of different CPUs discovered would trend upwards correspondingly. 

Or — and this fits, of course, with the actual situation we find (see Figure 2B) — most of the laptops would contain CPUs manufactured either by Intel or AMD. In this case, we would plot a line whose slope would change much more slowly, staying largely flat, in fact, after the CPUs from Intel and AMD were tallied.

The Core Rationale of Their Approach

Now consider Figure 3 (below), from the Gagler et al. 2022 paper. This shows the core rationale of their approach: tally the EC-classified enzyme “parts” within each of the major domains, and from metagenomes, and then plot that tally against the total EC numbers.

Figure 3 is used from Gagler et al. 2022 under Creative Commons License 4.0 (CC BY-NC-ND).

Figure 3 also shows their main finding. As the enzyme reaction space grows (on the horizontal axis — total EC numbers), so do the number of unique functions (on the vertical axis — EC numbers in each EC class).

The lesson that Gagler et al. 2022 draw from this discovery? The pattern is NOT due to material descent from a single common ancestor, LUCA. Indeed, under the heading, “Universality in Scaling of Enzyme Function Is Not Explained by Universally Shared Components,” they explain that material descent from LUCA would entail shared “microscale features,” meaning “specific molecules and reactions used by all life,” or “shared component chemistry across systems.” If we use the CPU / laptop analogy, this microscale commonality would be equivalent to finding CPUs from the same manufacturer, with the same internal logic circuits, in every laptop we examine.

But what Gagler et al. 2022 found was a macroscale pattern, “which does not directly correlate with a high degree of microscale universality,” and “cannot be explained directly by the universality of the underlying component functions.” In an accompanying news story, project co-author Chris Kempes, of the Santa Fe Institute, described their main finding in terms of functional synonyms: macroscale functions are required, but not the identical lower-level components:

“Here we find that you get these scaling relationships without needing to conserve exact membership. You need a certain number of transferases, but not particular transferases,” says SFI Professor Chris Kempes, a co-author on the paper. “There are a lot [of] ‘synonyms,’ and those synonyms scale in systematic ways.”

As Gagler et al. frame the point in the paper itself (emphasis added):

A critical question is whether the universality classes identified herein are a product of the shared ancestry of life. A limitation of the traditional view of biochemical universality is that universality can only be explained in terms of evolutionary contingency and shared history, which challenges our ability to generalize beyond the singular ancestry of life as we know it. …Instead, we showed here that universality classes are not directly correlated with component universality, which is indicative that it emerges as a macroscopic regularity in the large-scale statistics of catalytic functional diversity. Furthermore, EC universality cannot simply be explained due to phylogenetic relatedness since the range of total enzyme functions spans two orders of magnitude, evidencing a wide coverage of genomic diversity.

Sounds Like Intelligent Design

It is interesting to note that this paper was edited (for the PNAS) by Eugene Koonin of the National Center for Biotechnology Information. For many years, Koonin has argued in his own work that the putative “universality due to ancestry” premise of neo-Darwinian theory no longer holds, due in large measure to what he and others have termed “non-orthologous gene displacement” (NOGD). NOGD is a pervasive pattern of the use of functional synonyms — enzyme functions being carried out by different molecular actors — in different species. In 2016, Koonin wrote:

As the genome database grows, it is becoming clear that NOGD reaches across most of the functional systems and pathways such that there are very few functions that are truly “monomorphic”, i.e. represented by genes from the same orthologous lineage in all organisms that are endowed with these functions. Accordingly, the universal core of life has shrunk almost to the point of vanishing…there is no universal genetic core of life, owing to the (near) ubiquity of NOGD.

Universal functional requirements, but without the identity of material components — sounds like design.

 

Alas,OOL science just can't get a break

Origin of Life: The Problem of Cell Membranes

David Klinghoffer

 

 

Wow, the new Long Story Short video is out now, and I think it’s the best one yet — it’s amazingly clear and quite funny. You’ll want to share it with friends. Some past entries in the series have considered the problems associated with chemical evolution, or abiogenesis, how life could have emerged from non-life on the early Earth without guidance or design. The new video examines cell membranes, which some might imagine as little more than a soap bubble or an elastic balloon. This is VERY far from the case. 

To keep the cell alive, there’s an astonishing number of complex and contradictory things a cell membrane needs to do. If unassisted by intelligent design, how did the very first cell manage these tricks? It’s a puzzle, since “The membrane had to be extremely complex from the very BEGINNING, or life could never begin.” Some materialists have an answer: protocells, a simpler version of the simplest cells we know of today. But, asks Long Story, could a necessarily fragile, simpler cell survive without assistance from its environment, something like a hospital ICU? It seems not. If so, that makes any unguided scenario of abiogenesis a non-starter. We’ll have more to say in coming days about the science behind this.

 

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Yet more on why we can't take OOL science seriously

Origin of Life: Top Three Problems with Protocells

Rob Stadler

 

 

The latest video in the Long Story Short series was released this week on YouTube. The video explains how cell membranes in all of life display complexity that cannot be explained by purely natural processes. See my comments from yesterday, “New Animated Video: Cell Membranes by Natural Processes Alone?,” adding some supporting details to the argument. Here’s more.

 

As we uncover layer after layer of the astounding complexity of even the simplest forms of life, the origin-of-life research community increasingly relies upon their trump card: imaginary protocells that supposedly existed long ago and were dramatically simpler than existing life. As the story goes, modern life may indeed be very complex, but protocells used to be much simpler, and there was plenty of time for the complexity to develop.

Protocells conveniently fill the uncomfortably large gap between the simple molecules that can be produced by prebiotic processes and the staggering complexity of all extant life. But there are three major problems with the concept of protocells. These problems are all backed by strong empirical support, in sharp contrast with the concept of protocells.

A Coddling Environment

First, scientists have been working for decades to simplify existing life, trying to arrive at a minimal viable life form by jettisoning anything that is not essential from the simplest extant cells. The success of Craig Venter’s group is well known. Building on their efforts to produce synthetic life (“Synthia” or “Mycoplasma labritorium”) in 2010,^1,2 in 2016 they introduced the current record holder for the simplest autonomously reproducing cell (JVCI Syn3.0).³ With a genome of only 473 genes and 520,000 base pairs of DNA, JVCI Syn3.0 can reproduce autonomously, but it certainly isn’t robust. Keeping it alive requires a coddling environment — essentially a life-support system. To arrive at a slightly more stable and robust organism that reproduced faster, the team later added back 19 genes to arrive at JVCI Syn3A.⁴ When combined, this work provides an approximate boundary for the simplest possible self-replicating life. We are clearly approaching the limit of viable cell simplicity. It seems safe to conclude that at least 400 genes (and approximately 500,000 base pairs of DNA) are the minimum requirements to produce a self-replicating cell. 

Exporting to the Environment

Second, we know that the process of simplifying an existing cell by removing some of its functionality doesn’t actually simplify the overall problem — it only exports the required complexity to the environment. A complex, robust cell can survive in changing conditions with varying food sources. A simplified cell becomes dependent on the environment to provide a constant, precise stream of the required nutrients. In other words, the simplified cell has reduced ability to maintain homeostasis, so the cell can only remain alive if the environment takes on the responsibility for homeostasis. Referring to JVCI Syn3A, Thornberg et al. conclude, “Unlike most organisms, which have synthesis pathways for most of [their] building blocks, Syn3A has been reduced to the point where it relies on having to transport them in.”⁵ This implies that the environment must provide a continuous supply of more specific and complex nutrients. The only energy source that JVCI Syn3A can process is glucose,⁴ so the environment must provide a continuous supply of its only tolerable food. Intelligent humans can provide such a coddling life-support environment, but a prebiotic Earth could not. Protocells would therefore place untenable requirements on their environment, and the requirements would have to be consistently met for millions of years.

Striving for Simplicity

Third, we know that existing microbes are constantly trying to simplify themselves, to the extent that their environment will allow. In Richard Lenski’s famous E. coli experiment, the bacteria simplified themselves by jettisoning their ribose operons after a few thousand generations, because they didn’t need to metabolize ribose and they could replicate 2 percent faster without it, providing a selective advantage.⁶ Furthermore, Kuo and Ochman studied the well-established preference of prokaryotes to minimize their own DNA, concluding: “deletions outweigh insertions by at least a factor of 10 in most prokaryotes.”⁷ This means that existing life has been trying from the very start to be as simple as possible. Therefore, it is likely that extant life has already reached something close to the simplest possible form, unless experimenters like Lenski provide a coddling environment for a long duration that allows further simplification. But such an environment requires the intervention of intelligent humans to provide just the right ingredients, at the right concentrations, and at the right time. No prebiotic environment could do this. Therefore, scientists need not try to simplify existing life — we already have good approximations of the simplest form. Indeed, Mycoplasma genitalium has a genome of 580,000 base pairs and 468 genes⁸ whereas Craig Venter’s minimal “synthetic cell” JVCI Syn3.0 has a comparable genome of 520,000 base pairs and 473 genes.³

The data provide a clear picture: the surprising complexity of even the simplest forms of existing life — 500,00 base pairs of DNA — cannot be avoided and cannot be reduced unless intelligent agents provide a complex life-support environment. Because protocells would have had to survive and reproduce on a harsh and otherwise lifeless planet, protocells are not a viable concept. Protocells place origin-of-life researchers in a rather awkward position: relying upon an imaginary entity to sustain their belief that only matter and energy exist. 

References

1. Gibson DG et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 2010; 329:52–56. 
2. Gibson DG et al. Synthetic Mycoplasma mycoides JCVI-syn1.0 clone sMmYCp235-1, complete sequence. 2010. NCBI Nucleotide. Identifier: CP002027.1.
3. Hutchison CA III et al. Design and synthesis of a minimal bacterial genome. Science. 2016; 351: 1414.
4. Breuer et al. eLife 2019; 8:e36842. DOI: https://doi.org/10.7554/eLife.36842.
5. Thornburg ZR et al. Fundamental behaviors emerge from simulations of a living minimal cell. Cell 2022; 185: 345-360.
6. Cooper VS et al. Mechanisms causing rapid and parallel loss of ribose catabolism in evolving populations of Escherichia coli B. J Bacteriology 2001, 2834-2841.
7. Kuo, CH and Ochman H. Deletional bias across the three domains of life. Genome. Biol. Evol. 1:145–152.
8. Fraser CM et al. The minimal gene complement of Mycoplasma genitalium. Science. 1995; 270; 397-403.

 

Man to man is a wolf II

The ministry of truth is a thing?

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Byzantium:A brief history.

Byzantium (/bɪˈzæntiəm, -ʃəm/) or Byzantion (Greek: Βυζάντιον) was an ancient Greek city in classical antiquity that became known as Constantinople in late antiquity and Istanbul today. The Greek name Byzantion and its Latinization Byzantium continued to be used as a name of Constantinople sporadically and to varying degrees during the thousand year existence of the Byzantine Empire.^[1][2] Byzantium was colonized by Greeks from Megara in the 7th century BC and remained primarily Greek-speaking until its conquest by the Ottoman Empire in AD 1453.^[3]

 

Etymology

The etymology of Byzantium is unknown. It has been suggested that the name is of Thracian origin.^[4] It may be derived from the Thracian personal name Byzas which means "he-goat".^[5][6] Ancient Greek legend refers to the Greek king Byzas, the leader of the Megarian colonists and founder of the city.^[7] The name Lygos for the city, which likely corresponds to an earlier Thracian settlement,^[4] is mentioned by Pliny the Elder in his Natural History.^[8]

Byzántios, plural Byzántioi (Ancient Greek: Βυζάντιος, Βυζάντιοι, Latin: Byzantius; adjective the same) referred to Byzantion's inhabitants, also used as an ethnonym for the people of the city and as a family name.^[5] In the Middle Ages, Byzántion was also a synecdoche for the eastern Roman Empire. (An ellipsis of Medieval Greek: Βυζάντιον κράτος, romanized: Byzántion krátos).^[5] Byzantinós (Medieval Greek: Βυζαντινός, Latin: Byzantinus) denoted an inhabitant of the empire.^[5] The Anglicization of Latin Byzantinus yielded "Byzantine", with 15th and 16th century forms including Byzantin, Bizantin(e), Bezantin(e), and Bysantin as well as Byzantian and Bizantian.^[9]

The name Byzantius and Byzantinus were applied from the 9th century to gold Byzantine coinage, reflected in the French besant (d'or), Italian bisante, and English besant, byzant, or bezant.^[5] The English usage, derived from Old French besan (pl. besanz), and relating to the coin, dates from the 12th century.^[10]

Later, the name Byzantium became common in the West to refer to the Eastern Roman Empire, whose capital was Constantinople. As a term for the east Roman state as a whole, Byzantium was introduced by the historian Hieronymus Wolf only in 1555, a century after the last remnants of the empire, whose inhabitants continued to refer to their polity as the Roman Empire (Medieval Greek: Βασιλεία τῶν Ῥωμαίων, romanized: Basileía tōn Rhōmaíōn, lit. 'empire of the Romans'), had ceased to exist.^[11]

Other places were historically known as Byzántion (Βυζάντιον) – a city in Libya mentioned by Stephanus of Byzantium and another on the western coast of India referred to by the Periplus of the Erythraean Sea; in both cases the names were probably adaptations of names in local languages.^[5] Faustus of Byzantium was from a city of that name in Cilicia.^[5]

  History

 

The origins of Byzantium are shrouded in legend. Tradition says that Byzas of Megara (a city-state near Athens) founded the city when he sailed northeast across the Aegean Sea. The date is usually given as 667 BC on the authority of Herodotus, who states the city was founded 17 years after Chalcedon. Eusebius, who wrote almost 800 years later, dates the founding of Chalcedon to 685/4 BC, but he also dates the founding of Byzantium to 656 BC (or a few years earlier depending on the edition). Herodotus' dating was later favored by Constantine the Great, who celebrated Byzantium's 1000th anniversary between the years 333 and 334.^[12]

Byzanitium was mainly a trading city due to its location at the Black Sea's only entrance. Byzantium later conquered Chalcedon, across the Bosphorus on the Asiatic side.

The city was taken by the Persian Empire at the time of the Scythian campaign (513 BC) of King Darius I (r. 522–486 BC), and was added to the administrative province of Skudra.^[13] Though Achaemenid control of the city was never as stable as compared to other cities in Thrace, it was considered, alongside Sestos, to be one of the foremost Achaemenid ports on the European coast of the Bosphorus and the Hellespont.^[13]

Byzantium was besieged by Greek forces during the Peloponnesian War. As part of Sparta's strategy for cutting off grain supplies to Athens during their siege of Athens, Sparta took control of the city in 411 BC, to bring the Athenians into submission. The Athenian military later retook the city in 408 BC, when the Spartans had withdrawn following their settlement.^[14]

After siding with Pescennius Niger against the victorious Septimius Severus, the city was besieged by Roman forces and suffered extensive damage in AD 196.^[15] Byzantium was rebuilt by Septimius Severus, now emperor, and quickly regained its previous prosperity. It was bound to Perinthus during the period of Septimius Severus.^{[citation needed]} The strategic and highly defensible (due to being surrounded by water on almost all sides) location of Byzantium attracted Roman Emperor Constantine I who, in AD 330, refounded it as an imperial residence inspired by Rome itself, known as Nova Roma. Later the city was called Constantinople (Greek Κωνσταντινούπολις, Konstantinoupolis, "city of Constantine").

This combination of imperialism and location would affect Constantinople's role as the nexus between the continents of Europe and Asia. It was a commercial, cultural, and diplomatic centre and for centuries formed the capital of the Byzantine Empire, which decorated the city with numerous monuments, some still standing today. With its strategic position, Constantinople controlled the major trade routes between Asia and Europe, as well as the passage from the Mediterranean Sea to the Black Sea. On May 29, 1453, the city fell to the Ottoman Turks, and again became the capital of a powerful state, the Ottoman Empire. The Turks called the city "Istanbul" (although it was not officially renamed until 1930); the name derives from "eis-ten-polin" (Greek: "to-the-city"). To this day it remains the largest and most populous city in Turkey, although Ankara is now the national capital.

Emblem

 

By the late Hellenistic or early Roman period (1st century BC), the star and crescent motif was associated to some degree with Byzantium; even though it became more widely used as the royal emblem of Mithradates VI Eupator (who for a time incorporated the city into his empire).^[16]

Some Byzantine coins of the 1st century BC and later show the head of Artemis with bow and quiver, and feature a crescent with what appears to be an eight-rayed star on the reverse. According to accounts which vary in some of the details, in 340 BC the Byzantines and their allies the Athenians were under siege by the troops of Philip of Macedon. On a particularly dark and wet night Philip attempted a surprise attack but was thwarted by the appearance of a bright light in the sky. This light is occasionally described by subsequent interpreters as a meteor, sometimes as the moon, and some accounts also mention the barking of dogs. However, the original accounts mention only a bright light in the sky, without specifying the moon.^[a][b] To commemorate the event the Byzantines erected a statue of Hecate lampadephoros (light-bearer or bringer). This story survived in the works of Hesychius of Miletus, who in all probability lived in the time of Justinian I. His works survive only in fragments preserved in Photius and the tenth century lexicographer Suidas. The tale is also related by Stephanus of Byzantium, and Eustathius.

Devotion to Hecate was especially favored by the Byzantines for her aid in having protected them from the incursions of Philip of Macedon. Her symbols were the crescent and star, and the walls of her city were her provenance.^[19]

It is unclear precisely how the symbol Hecate/Artemis, one of many goddesses^[c] would have been transferred to the city itself, but it seems likely to have been an effect of being credited with the intervention against Philip and the subsequent honors. This was a common process in ancient Greece, as in Athens where the city was named after Athena in honor of such an intervention in time of war.

Cities in the Roman Empire often continued to issue their own coinage. "Of the many themes that were used on local coinage, celestial and astral symbols often appeared, mostly stars or crescent moons."^[21] The wide variety of these issues, and the varying explanations for the significance of the star and crescent on Roman coinage precludes their discussion here. It is, however, apparent that by the time of the Romans, coins featuring a star or crescent in some combination were not at all rare.

People

 

• Homerus, tragedian, lived in the early 3rd century BC
• Philo, engineer, lived c. 280 BC–c. 220 BC
• Epigenes of Byzantium, astrologer, lived in the 3rd–2nd century BC
• Aristophanes of Byzantium, a scholar who flourished in Alexandria, 3rd–2nd century BC
• Myro, a Hellenistic female poet

See also

 

• Constantinople, which details the history of the city before 1453
  • Fall of Constantinople (Turkish conquest of 1453)
• Istanbul, which details the history of the city from 1453 on, and describes the modern city
• Sarayburnu, which is the geographic location of ancient Byzantium
• Timeline of Istanbul history

Notes

1. 
   

3. "In 324 Byzantium had a number of operative cults to traditional gods and goddesses tied to its very foundation eight hundred years before. Rhea, called "the mother of the gods" by Zosimus, had a well-ensconced cult in Byzantium from its very foundation. [...] Devotion to Hecate was especially favored by the Byzantines [...] Constantine would also have found Artemis-Selene and Aphrodite along with the banished Apollo Zeuxippus on the Acropolis in the old Greek section of the city. Other gods mentioned in the sources are Athena, Hera, Zeus, Hermes, and Demeter and Kore. Even evidence of Isis and Serapis appears from the Roman era on coins during the reign of Caracalla and from inscriptions." ^[20]

References

1. 
   

21. Molnar, Michael R. (1999). The Star of Bethlehem. Rutgers University Press. p. 48.

Sources

• Balcer, Jack Martin (1990). "BYZANTIUM". In Yarshater, Ehsan (ed.). Encyclopædia Iranica, Volume IV/6: Burial II–Calendars II. London and New York: Routledge & Kegan Paul. pp. 599–600. ISBN 978-0-71009-129-1.
• Harris, Jonathan, Constantinople: Capital of Byzantium (Hambledon/Continuum, London, 2007). ISBN 978-1-84725-179-4
• Jeffreys, Elizabeth and Michael, and Moffatt, Ann, Byzantine Papers: Proceedings of the First Australian Byzantine Studies Conference, Canberra, 17–19 May 1978 (Australian National University, Canberra, 1979).
• Istanbul Historical Information – Istanbul Informative Guide To The City. Retrieved January 6, 2005.
• The Useful Information about Istanbul Archived 2007-03-15 at the Wayback Machine. Retrieved January 6, 2005.
• The Oxford Dictionary of Byzantium (Oxford University Press, 1991) ISBN 0-19-504652-8
• Yeats, William Butler, "Sailing to Byzantium",

"In 340 BC, however, the Byzantines, with the aid of the Athenians, withstood a siege successfully, an occurrence the more remarkable as they were attacked by the greatest general of the age, Philip of Macedon. In the course of this beleaguerment, it is related, on a certain wet and moonless night the enemy attempted a surprise, but were foiled by reason of a bright light which, appearing suddenly in the heavens, startled all the dogs in the town and thus roused the garrison to a sense of their danger. To commemorate this timely phenomenon, which was attributed to Hecate, they erected a public statue to that goddess [...]"^[17]

"If any goddess had a connection with the walls in Constantinople, it was Hecate. Hecate had a cult in Byzantium from the time of its founding. Like Byzas in one legend, she had her origins in Thrace. Since Hecate was the guardian of "liminal places," in Byzantium small temples in her honor were placed close to the gates of the city. Hecate's importance to Byzantium was above all as deity of protection. When Philip of Macedon was about to attack the city, according to the legend she alerted the townspeople with her ever-present torches, and with her pack of dogs, which served as her constant companions. Her mythic qualities thenceforth forever entered the fabric of Byzantine history. A statue known as the 'Lampadephoros' was erected on the hill above the Bosphorous to commemorate Hecate's defensive aid."^[18]

Speake, Jennifer (2003). Literature of Travel and Exploration: A to F. p. 160. ISBN 9781579584252.

Kazhdan, A. P.; Epstein, Ann Wharton (February 1990). Change in Byzantine Culture in the Eleventh and Twelfth Centuries. University of California Press. p. 1. ISBN 9780520069626. Byzantion term remained used for constantinople.

The Rise of the Greeks. Orion Publishing Group. 2012. p. 22. ISBN 978-1780222752.

Janin, Raymond (1964). Constantinople byzantine: dévelopment urbain et répertoire topographique (in French). Paris: Institut Français d'Études Byzantines. pp. 10–11.

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The dominion of mathematics and the design debate.

Unexplained — Maybe Unexplainable — Numbers Control the Universe

Evolution News @DiscoveryCSC

 

In Carl Sagan’s Contact, the extraterrestrials embedded a message in the irrational number pi (the circumference of a circle divided by its radius). But some other numbers are critical to the structure of our universe too — and why they are critical does not make obvious sense.

• Perhaps the most fundamental and mysterious one is the fine structure constant of the universe:

A seemingly harmless, random number with no units or dimensions has cropped up in so many places in physics and seems to control one of the most fundamental interactions in the universe.

Its name is the fine-structure constant, and it’s a measure of the strength of the interaction between charged particles and the electromagnetic force. The current estimate of the fine-structure constant is 0.007 297 352 5693, with an uncertainty of 11 on the last two digits. The number is easier to remember by its inverse, approximately 1/137.

If it had any other value, life as we know it would be impossible. And yet we have no idea where it comes from. 

PAUL SUTTER, “LIFE AS WE KNOW IT WOULD NOT EXIST WITHOUT THIS HIGHLY UNUSUAL NUMBER” AT SPACE.COM (MARCH 24, 2022)

Many famous scientists have reflected on 1/137:

The brilliant physicist Richard Feynman (1918-1988) famously thought so, saying there is a number that all theoretical physicists of worth should “worry about”. He called it “one of the greatest damn mysteries of physics: a magic number that comes to us with no understanding by man”…

What’s special about alpha is that it’s regarded as the best example of a pure number, one that doesn’t need units. It actually combines three of nature’s fundamental constants – the speed of light, the electric charge carried by one electron, and the Planck’s constant, as explains physicist and astrobiologist Paul Davies to Cosmos magazine. Appearing at the intersection of such key areas of physics as relativity, electromagnetism and quantum mechanics is what gives 1/137 its allure. 

PAUL RATNER, “WHY THE NUMBER 137 IS ONE OF THE GREATEST MYSTERIES IN PHYSICS” AT BIG THINK (OCTOBER 31, 2018)

First Question to the Devil

Nobelist Wolfgang Pauli (1945) is said to have remarked, “When I die, my first question to the devil will be: What is the meaning of the fine structure constant?” At any rate, he thought about it a great deal during his life.

University of Nottingham physics professor Laurence Eaves thinks the number 1/137 would be good for starting communication with intelligent aliens as they would be likely to know about it and to realize they were dealing with other intelligent entities.

• Here’s another thought-provoking number. Consider the irrational number known as phi (ϕ) or the Golden Ratio. Jordan Ellenberg author of Shape: The Hidden Geometry of Information, Biology, Strategy, Democracy, and Everything Else (2021):

Among the mysteries of the irrationals, one number holds a special place: the so-called golden ratio. The golden ratio’s value is about 1.618 (but not exactly 1.618, since then it would be the ratio 1,618/1,000, and therefore not irrational) and it’s also referred to by the Greek letter φ, which is pronounced “fee” if you’re a mathematician and “fie” if you are in a fraternity. If you want an exact description, the golden ratio can be expressed as (1/2)(1+√5.)

JORDAN ELLENBERG, “THE MOST IRRATIONAL NUMBER” AT SLATE (JUNE 8, 2021)

The “Divine Proportion”

We find this number everywhere too:

The golden ratio is sometimes called the “divine proportion,” because of its frequency in the natural world. The number of petals on a flower, for instance, will often be a Fibonacci number. The seeds of sunflowers and pine cones twist in opposing spirals of Fibonacci numbers. Even the sides of an unpeeled banana will usually be a Fibonacci number — and the number of ridges on a peeled banana will usually be a larger Fibonacci number.

RESOURCE LIBRARY, “THE GOLDEN RATIO” AT NATIONAL GEOGRAPHIC SOCIETY

• Then there is pi (π), which (outside of Carl Sagan’s novel and film) burbles on forever without forming a pattern, yet it is fundamental in nature too.

Read the rest at Mind Matters News, published by Discovery Institute’s Bradley Center for Natural and Artificial Intelligence.

 

 

A brain than can know/A world that can be known and the design debate.

How Does the Intelligibility of Nature Point to Design?

Bruce Gordon

 

Editor’s note: This article is an excerpt from the newly released book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. 

Albert Einstein (1879–1955) famously remarked that “the eternal mystery of the world is its comprehensibility…[t]he fact that it is comprehensible is a miracle.” Similarly, the mathematical physicist Eugene Wigner (1902–1995) opined that “[t]he miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve.” 

As these remarks highlight, the intelligibility of the universe to the human mind requires explanation in two respects. The first is ontological: Why is nature ordered in such a way that it can be understood? The second is epistemological: Why is the human mind able to gain understanding of the natural order? In the past, these questions did not provoke the puzzlement they do today. Let’s get some historical perspective on the rise of modern science and the current milieu before we examine why a metaphysically naturalistic worldview provides no good answers to these questions, and why theism, which understands the universe as the product of intelligent design, is the only metaphysical context in which the existence and intelligibility of nature has an explanation.

Historical Perspective

For science to be possible, there must be order present in nature, and it has to be discoverable by the human mind. But why should either of these conditions be met? Historically, while there were temporary manifestations of systematic research into nature in ancient Greece and early Islam, and isolated discoveries elsewhere, the seeds of modern science first came to concentrated and sustained fruition in Western culture before its methodologies and achievements were disseminated throughout the world. 

This lasting and world-changing development emerged in the context of the Judeo-Christian worldview that permeated medieval Europe. What drove it was a deeply entrenched society-wide conception of the universe as the free and rational creation of God’s mind so that human beings, as rational creatures made in God’s image, were capable of searching out and understanding a divinely ordered reality. The freedom of God’s creative will meant that this order could not be abstractly deduced ― it had to be discovered through observation and experiment ― but God’s stable and faithful character guaranteed it had a rational structure that diligent study could reveal. This theological foundation gave solid answers to ontological and epistemological questions concerning the intelligibility of the universe, but as the quotes from Einstein and Wigner make clear, this foundation had been lost by the middle of the 20th century. Why?

Efficient and Material Causes

Some see it as the outworking of the 17th-century mechanical philosophy that sought to explain all natural phenomena in terms of material contact mechanisms. On this view, mechanical philosophy conceptually reduced scientific causality to efficient and material causes, purging Aristotelian notions of formal and final causality from science. This is perhaps plausible methodologically, but not metaphysically. The conception of mechanism in the mechanical philosophy retained formal causes in their design and final causes in the purpose they were created to serve. The break with Aristotle arose from the fact that, in the conception of the theistic and deistic mechanical philosophers, design and purpose were transcendently imposed rather than immanently active, so the search for scientific explanations turned to the intelligent implementation of efficient material mechanisms. The purge of any sense of design and purpose from the “scientific” conception of nature is due to the late-19th-century rise of Darwinian philosophy, which sees the mechanisms of nature as brute facts and the course of their development as completely blind and purposeless.

Under the Aegis of Naturalism

It is Darwinism, so conceived, that renders the existence of mathematically describable regularities in nature and their intelligibility to the human mind (itself conceived as the accidental result of blind processes) as such a surprise, for it assumes naturalism ― the self-contained character of nature and the denial of supernaturalism ― as the context for science. Under the aegis of naturalism, there can be no expectation that nature is regular in a way that allows presently operative causes to be projected into the past to explain the current state of the universe or into the future to predict its development. The absence of any sufficient cause to explain why nature exists leaves the philosophical naturalist with no reason to think that what does exist should be ordered, or that any order he finds should be projectable into the past or the future. 

By denying transcendence and defaulting to a conception of the universe as a closed and ultimately arbitrary system of causes and effects, naturalism makes science the uncanny enterprise on which Einstein and Wigner remarked. On the other hand, the Judeo-Christian worldview recognizes that nature exists and is regular not because it is closed to divine activity, but because (and only because) divine causality is operative. It is only because nature is a creation and thus not a closed system of causes and effects that it exists in the first place and exhibits the regular order that makes science possible. God’s existence and action is not an obstacle to science; it’s what makes it possible.