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Friday 28 May 2021

Why Darwinism's 'simple beginning just keeps receding.

 

Zip It: How Cells Repair Leaking Membranes

Evolution News DiscoveryCSC

Membrane repair would have been necessary with the first cell. If by a most fantastic miracle scenario — against all probability — a protocell emerged from the primordial soup, it would be all over quickly if the membrane sprang a leak. 

Origin-of-life theorists often assume that membranes would spontaneously form naturally around protocells by the properties of lipid self-organization. That, however, is only the beginning of their challenges. Membranes need channels for active transport to control what goes in and out. They also need repair mechanisms if they break. If by inconceivable chance miracles those properties also emerged along with the lucky contents for life inside the membrane, they would never be inherited if they were not preserved in the genetic code. But even that is not enough. Along with code, machinery must be present to translate the code into other machines that know what to do when a membrane breaks. Unwatched membranes are vulnerable to leaks, and they don’t care. Without foresight and oversight, protocells would be like bubbles that pop in due time. Too bad for those hard-won living ingredients inside.

Fixing a Hole

A paper in the EMBO Journal by Yan Zhen et al., “Sealing holes in cellular membranes,” describes how cells actively monitor and repair leaks. The four authors identify multiple mechanisms for membrane repair. The resemblance to Michael Behe’s irreducibly complex blood clotting cascade (Darwin’s Black Box, Chapter 4) is uncanny, yet this is a leak-patching system an order of magnitude smaller!

The bilayered membranes of eukaryotic cells are vital to their very existence, with the plasma membrane separating the cells from their surroundings, and the endomembranes enclosing the various organelles. It is crucial that these membranes are intact so that only gated transport of molecules and ions across them can occur. Defective membrane sealing is indeed associated with a large number of diseases, including myopathies, central and peripheral neurological disorders, and coronary diseases (Cooper & McNeil, 2015). Sealing of holes in membranes is therefore of great importance in biology, both during biogenesis of double‐membrane organelles and as response to membrane damage…. The molecular and cellular mechanisms that have evolved to seal such holes will be discussed in this review.  [Emphasis added.]

Ah, yes, they “have evolved.” It was so simple. A chance miracle here, another one there; what’s the issue? And yet the diagrams and descriptions of actual mechanisms for maintaining membrane integrity are mind-boggling in their efficiency and complexity. 

Membrane sealing is an ongoing issue for a cell. The authors state that 20-30 percent of muscle cells and 6 percent of skin cells present transient leaks in their membranes that must be sealed promptly, or else serious diseases can occur.

Self-Sealing and Vesicles

For a hole only a few nanometers in size, the properties of lipid attraction allow for spontaneous sealing. Anything larger requires help, though, because membranes are under tension. A hole can quickly rip a stretched cell apart. The cell has at least three ways to reduce membrane tension, the authors say, allowing spontaneous sealing to proceed. Larger holes can be patched by vesicles, which are small lipid-surrounded sacks. A vesicle from outside can cover the hole and merge its lipids with the plasma membrane. Or the membrane can bud outward to bring the intact portions together. Some scientists think that “fusion causes release of an enzyme that promotes membrane sealing.” Imagine a bandage that could merge with your skin!

The cell must have ways to know that a leak has begun. A rapid influx of Ca2+ ions triggers a “simple yet powerful mechanism for detection of membrane integrity.” This, however, requires the presence of proteins that bind to the calcium ions so that they can trigger mechanisms that “promote membrane sealing by membrane fusion, fission or tension reduction.”

What happens to the vesicles after repair has been accomplished? Outside the cell, macrophages can engulf them. Inside, lysomes (the cell’s trash collectors) can engulf them. 

Even though membrane repair has mostly been described as a cell autonomous mechanism, muscle cells, which are particularly prone to damage of their plasma membrane, can also engage neighbouring macrophages to pinch off damaged portions of the muscle cell plasma membrane (Middel et al, 2016) (Fig 1F). How macrophage‐mediated removal of the damaged plasma membrane can proceed in a way that preserves membrane integrity still remains to be resolved.

Enzyme Army

Table 1 in the paper lists at least 16 proteins and protein families that promote membrane sealing in four categories of damage. Annexins, for instance, gather at the site of damage and “assemble into multimeric structures that physically cap the hole in the membrane.” Another protein, named Dysferlin, “Accumulates phosphatidylserine at the site of membrane damage, as an ‘eat‐me’ signal for macrophages.” Dysferlin also “interacts with some annexins” indicating that membrane repair proteins are not superheroes acting alone, but form networks of players that work together. Cooperation between proteins that can solve problems multiplies exponentially the improbability of their spontaneous emergence by unguided natural processes. Here’s another example to show the complexity involved:

Synaptotagmins are integral membrane proteins that function as Ca2+sensors that mediate membrane fusion. Among these, Synaptotagmin‐7 (SYT7) has been found to be particularly important for membrane repair. The cytosolic part of SYT7 contains two Ca2+ ‐ and phospholipid‐binding C2 domains that sense cytosolic Ca2+and mediate interactions with membranes. Like other members of the Synaptotagmin family, SYT7 regulates formation of SNARE complexes that drive membrane fusion and thus transduces Ca2+ sensing into membrane fusion ….

The authors go on to describe other proteins that can sense the damage and take appropriate actions. For instance, PDCD6 is a small calcium-binding sensor with big friends.

One of the interacting partners of PDCD6 is ALIX (PDCD6IP), a scaffolding protein involved in diverse cellular functions. ALIX also binds Ca2+, albeit with lower affinity than PDCD6. Injury‐triggered influx of Ca2+ causes accumulation of PDCD6 at the site of injury, and PDCD6 in turn recruits ALIX. ALIX then recruits components of the ESCRT machinery that mediates membrane repair by outward budding and fission of the damaged membrane area….

Not Small Players

Uniprot shows that PDCD6 has 865 amino acids. These are not small players! A whole squadron of machines takes part in healing membrane holes, just like an army of players is required in the blood clotting cascade to repair breaks in blood vessels. There are additional machines involved in repairing internal membranes surrounding organelles and the nucleus. Space forbids discussion here of the ESCRT and SNARE proteins and other players; those interested can read more in the open-access paper or just look at the tables and diagrams to be impressed. But why so many players? The authors refer to backup plans and redundancy: 

There is strong evidence that multiple mechanisms have evolved to seal holes in membranes, and there may be good reasons why separate mechanisms exist. Firstly, because membrane integrity is so crucial for cellular viability and functions, the existence of multiple sealing mechanisms could ensure successful sealing even if one mechanism fails. Secondly, the different mechanisms are optimized for sealing of different types of holes …. It is also plausible that additional mechanisms of membrane sealing exist, which have not been characterized yet.

“It Evolved”

Membrane repair is a key emergency operation for a cell. Just like countries with different military branches for external threats and police agencies for internal threats, cells come well equipped to handle breaches to their security. Saying these systems “have evolved” explains nothing. Something had the foresight to know these systems would be necessary for life and health. Something has the oversight to ensure their successful operation. The irreducible complexity touched on with this brief look at membrane repair provides additional and powerful evidence for intelligent design

Saturday 22 May 2021

From trash to treasure?

Noncoding “Junk” DNA Is Important for Limb Formation

Casey Luskin

A 2021 article in Nature, “Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator,” reports important new functions for non-coding or “junk” DNA that underlie limb formation. Before we get to the paper itself, consider a description of it on the Proceedings of the National Academy of Sciences “Journal Club” blog. The latter describes the research in terms that sound like they could have come directly from an intelligent design source: 

Genes that code for proteins make up only about 2% of the human genome. Many researchers once dismissed the other 98% of the genome as “junk DNA,” but geneticists now know these noncoding regions help to regulate the activity of the 20,000 or so protein-coding genes identified.

A new study in Nature underscores just how important noncoding DNA can be for human development. The authors show that deletions in a noncoding region of DNA on chromosome 2 cause severe congenital limb abnormalities. This is the first time a human disease has been definitively linked to mutations in noncoding DNA, says lead author Stefan Mundlos, head of the development and disease research group at the Max Planck Institute for Molecular Genetics in Berlin, Germany.

“Severe Congenital Limb Malformation” 

The technical paper in Nature describes the research. The investigators examined the chromosomes of people who had naturally occurring limb malformation, and found that these people had deletions of DNA encoding long non-coding RNA sequences (lncRNAs) from human chromosome 2. They deleted corresponding DNA sequences in mice and found similar “severe congenital limb malformation,” suggesting these lncRNA sequences are functionally important:

Here we show that genetic ablation of a lncRNA locus on human chromosome 2 causes a severe congenital limb malformation. We identified homozygous 27–63-kilobase deletions located 300 kilobases upstream of the engrailed-1 gene (EN1) in patients with a complex limb malformation featuring mesomelic shortening, syndactyly and ventral nails (dorsal dimelia). Re-engineering of the human deletions in mice resulted in a complete loss of En1expression in the limb and a double dorsal-limb phenotype that recapitulates the human disease phenotype. Genome-wide transcriptome analysis in the developing mouse limb revealed a four-exon-long non-coding transcript within the deleted region, which we named Maenli. Functional dissection of the Maenli locus showed that its transcriptional activity is required for limb-specific En1 activation in cis, thereby fine-tuning the gene-regulatory networks controlling dorso-ventral polarity in the developing limb bud. 

In the discussion, the article explains how important it is that we seek to understand the key functions of non-coding DNA sequences that encode lncRNAs:

In the era of whole-genome sequencing, the findings described here underscore the need for a systematic annotation and functional characterization of lncRNA loci to interpret and classify non-coding genetic variants. They highlight the importance of elucidating the complex diversity of lncRNA modes of action to assess their role in organ development and disease.

Over 130,000 Functional “Junk DNA” Elements!

So just how are we progressing in the task of determining the functions of non-coding DNA elements? Some defenders of evolutionary orthodoxy would have us believe that we’ve only found a handful of non-coding DNA sequences that have function — exceptions to the rule that non-coding DNA is usually useless junk. Another 2021 article in Nature shows why it’s no longer tenable for evolutionists to hide behind such an argument from ignorance. The article explains that over 130,000 functional “genomic elements, previously called junk DNA” have now been discovered, highlighting how important these “junk” segments have turned out to be:

[I]t is now appreciated that the majority of functional sequences in the human genome do not encode proteins. Rather, elements such as long non-coding RNAs, promoters, enhancers and countless gene-regulatory motifs work together to bring the genome to life. Variation in these regions does not alter proteins, but it can perturb the networks governing protein expression With the HGP draft in hand, the discovery of non-protein-coding elements exploded. So far, that growth has outstripped the discovery of protein-coding genes by a factor of five, and shows no signs of slowing. Likewise, the number of publications about such elements also grew in the period covered by our data set. For example, there are thousands of papers on non-coding RNAs, which regulate gene expression.

The article also observes that prior to the Human Genome Project, which was completed in 2003, there was “great debate” over whether it was “worth mapping the vast non-coding regions of genome that were called junk DNA, or the dark matter of the genome.” Under a paradigm informed by intelligent design, debates over whether to investigate junk DNA would have ended much sooner with an emphatic Yes!, furthering our knowledge of genetics and medicine. How much sooner would these 130,000+ “genomic elements, previously called junk DNA” have been uncovered if an ID paradigm had been governing biology research? 


Monday 17 May 2021

Yet more on the sacred name in the N.T

YHWH in the New Testament:

This article is a English version of a Italian article published on the catholic magazine, edited from Dehonian friars, "Rivista Biblica", year XLV, n. 2, April-June 1997, p. 183-186. Bologna, Italy.


 

For a long time it was thought that the divine Tetragrammaton YHWH, in Hebrew written with the letters YHWH (which recurs over 6800 times in the Hebrew text of the Old Testament) did not appear in the original writings of the New Testament. In its place it was thought that the writers of the New Testament had used the Greek word for LORD, KYRIOS. However, it seems that such an opinion is wrong. Here below are some factors to consider:

1) The Tetragrammaton in the Greek Version of Old Testament, the Septuagint (LXX).

One of the reasons produced to support the above mentioned opinion was that the LXX substituted YHWH (YHWH) with the term KYRIOS, (kurios) which was the equivalent Greek of the Hebrew word ADONAY used by some Hebrews when they met the Tetragrammaton during the Bible reading.

However, recent discoveries have shown that the practice of substituted in the LXX YHWH with KYRIOS started in a much later period in comparison with the beginning of that version. As a matter of fact, the older copies of the LXX keep the Tetragrammaton written in Hebrew characters in the Greek text. (See App. 1)

Girolamo, the translator of the Latin Vulgate confirms this fact. In the prologue of the books of Samuel and Kings he wrote: "In certain Greek volumes we still find the Tetragrammaton of God's name expressed in ancient characters". And in a letter written in Rome in the year 384 it says: "God's name is made up of four letters; it was thought ineffable, and it is written with these letters: iod, he, vau, he (YHWH). But some have not been able to decipher it because of the resemblance of the Greek letters and when they found it in Greek books they usually read it PIPI (pipi)". S. Girolamo, Le Lettere, Rome, 1961, vol.1, pp.237, 238; compare J.P.Migne, Patrologia Latina, vol.22, coll.429, 430.

Around 245 C.E., the noted scholar Origen produced his Hexapla, a six-column reproduction of the inspired Hebrew Scriptures: (1) in their original Hebrew and Aramaic, accompanied by (2) a transliteration into Greek, and by the Greek versions of (3) Aquila, (4) Symmachus, (5) the Septuagint, and (6) Theodotion. On the evidence of the fragmentary copies now known, Professor W. G. Waddell says: "In Origen's Hexapla . . . the Greek versions of Aquila, Symmachus, and LXX all represented JHWH by PIPI; in the second column of the Hexapla the Tetragrammaton was written in Hebrew characters." - The Journal of Theological Studies, Oxford, Vol. XLV, 1944, pp. 158, 159. Others believe the original text of Origen's Hexapla used Hebrew characters for the Tetragrammaton in all its columns. Origen himself stated that "in the most accurate manuscripts THE NAME occurs in Hebrew characters, yet not in today's Hebrew [characters], but in the most ancient ones".

A biblical magazine declare: "In pre-Christian Greek [manuscripts] of the OT, the divine name was not rendered by 'kyrios' as has often been thought. Usually the Tetragram was written out in Aramaic or in paleo-Hebrew letters. . . . At a later time, surrogates such as 'theos' [God] and 'kyrios' replaced the Tetragram . . . There is good reason to believe that a similar pattern evolved in the NT, i.e. the divine name was originally written in the NT quotations of and allusions to the OT, but in the course of time it was replaced by surrogates". - New Testament Abstracts, March 1977, p. 306.

Wolfgang Feneberg comments in the Jesuit magazine Entschluss/Offen (April 1985): "He [Jesus] did not withhold his father's name YHWH from us, but he entrusted us with it. It is otherwise inexplicable why the first petition of the Lord's Prayer should read: 'May your name be sanctified!'" Feneberg further notes that "in pre-Christian manuscripts for Greek-speaking Jews, God's name was not paraphrased with kýrios [Lord], but was written in the tetragram form in Hebrew or archaic Hebrew characters. . . . We find recollections of the name in the writings of the Church Fathers".

Dr. P.Kahle says: "We now know that the Greek Bible text [the Septuagint] as far as it was written by Jews for Jews did not translate the Divine name by kyrios, but the Tetragrammaton written with Hebrew or Greek letters was retained in such MSS [manuscripts]. It was the Christians who replaced the Tetragrammaton by kyrios, when the divine name written in Hebrew letters was not understood any more". - The Cairo Geniza, Oxford, 1959, p. 222.

Further confirmation comes from The New International Dictionary of New Testament Theology, that says: "Recently discovered texts doubt the idea that the translators of the LXX have rendered the Tetragrammaton JHWH with KYRIOS. The most ancient mss (manuscripts) of the LXX today available have the Tetragrammaton written in Hebrew letters in the Greek text. This was custom preserved by the later Hebrew translator of the Old Testament in the first centuries (after Christ)". Vol.2, pag.512.

Consequently, we can easily deduce that if the writers of NT in their quotations of the OT used the LXX they would surely have left the Tetragrammaton in their writings the way it recurred in the Greek version of the OT. To confirm the correctness of this conclusion it is interesting to note the following declaration made before the finding of the manuscripts proving that the LXX originaly continued the Tetragrammaton:

"If that version (LXX) would have kept the term (YHWH), or had used the Greek term for JEHOVAH and another for ADONAY, such a use would have surely been followed in the discourses and in the reasonings of the NT. Therefore our Lord, in quoting the 110th Psalms, insteand of saying: 'The LORD has said to my LORD' could have said: "JEHOVA has said to ADONI". Supposing that a Christian student was translating in Hebrew the Greek Testament: every time that he met the word KYRIOS, he should have had to consider if in the context there was something that indicated the true Hebrew correspondent; and this is the difficulty that would have arisen in translating the NT in whatever language if the name JEHOVAH would have been left in the Old Testament (LXX). The Hebrew scriptures would have constituted a standard for many passages: every time that the expression "the LORD's angel" recurs, we know that the term LORD represents JEHOVA; we could come to a similar conclusion for the expression "the LORD's word", according to the precedent established in the OT; and so it is in the case of the name "the LORD of armies". On the contrary, when the expression "my LORD" or "our LORD" recurs, we should know that the term JEHOVA would be inadmissible, when instead the words ADONAY or ADONI should be used". R.B.Girdlestone, Synonyms of the Old Testament, 1897, p.43.

For a stronger support of this argument there are the words of the professor George Howard, of the University of Georgia (U.S.A.) who observes: "When the Septuagint Version that the New Testament Church used and quoted, contained the Divine Name in Hebrew characters, the writers of the New Testament included without doubt the Tetragrammaton in their quotations". Biblical Archeology Review, March 1978, p.14.

Consequently several translators of the NT have left the Divine Name in the quotations from the OT made by the New Testament writers. It can be noted, for example the versions of Benjamin Wilson, of Andrè Chouraqui, of Johann Jakob Stolz, of Hermann Heinfetter,in Efik, Ewe, Malgascio and Alghonchin languages.

2)The Tetragrammaton in Hebrew version of the NT.

As many know, the first book of the NT, the gospel of Matthew was written in Hebrew. The proof of this is found in the work of Girolamo De viris inlustribus, chap. 3, where he writes:

"Matthew, that is also Levi, that became an apostle after having been a tax collector, was the first to write a Gospel of Christ in Judea in the Hebrew language and Hebrew characters, for the benefit of those who where circumcised that had believed. It's not know with enough certainly who had then translated it in Greek. However the Hebrew one it self is preserved till this day in the Library at Cesarea, that the martyr Pamphilus collected so accurately. The Nazarenes of the Syrian city of Berea that use this copy have also allowed me to copy it". From the Latin text edited by E.C.Richardson, published in the series Texte und Untersuchungen zur Geschicte der altchristlichen Literatur, vol.14, Lipsia, 1986, pp.8,9.

External evidence to the effect that Matthew originally wrote this Gospel in Hebrew reaches as far back as Papias of Hierapolis, of the second century a.C. Eusebius quoted Papias as stating: "Matthew collected the oracles in the Hebrew language". - The Ecclesiastical History, III, XXXIX, 16. Early in the third century, Origen made reference to Matthew's account and, in discussing the four Gospels, is quoted by Eusebius as saying that the "first was written . . . according to Matthew, who was once a tax-collector but afterwards an apostle of Jesus Christ, . . . in the Hebrew language". - The Ecclesiastical History, VI, XXV, 3-6.

Was this really Aramaic? Not according to documents mentioned by George Howard. He wrote: "This supposition was due primarily to the belief that Hebrew in the days of Jesus was no longer in use in Palestine but had been replaced by Aramaic. The subsequent discovery of the Dead Sea Scrolls, many of which are Hebrew compositions, as well as of other Hebrew documents from Palestine from the general time period of Jesus, now show Hebrew to have been alive and well in the first century".

It is therefore natural to conclude that when Matthew quoted passages from the OT in which the Tetragrammaton appeared (thing that occurred both in the Hebrew OT and in the Greek one then available) he would have surely left YHWH in his gospel as no Jew ever dared to take away the Tetragrammaton from the Hebrew text of the Holy Scriptures.

To confirm this there are at least 27 Hebrew versions of the NT that present the Tetragrammaton in the quotations of the OT or where the text requires it. (see app.2) Three of these are the versions of F.Delitzsch, of I.Salkinson & C.D.Ginsburg , of the United Bible Societies, ed.1991 and of Elias Hutter.

3) The Tetragrammaton in the Christian Scriptures according to the Babylonian Talmud.

The first part of this Jewish work is called Shabbath (Sabbath) and it contains an immense code of rules that establishes what could have been done of a Sabbath. Part of it deals with if on the Sabbath day Biblical manuscripts could be saved from the fire, and after it reads:

"The text declares: 'The white spaces ("gilyohnim") and the books of the Minim, can't be saved from the fire'. Rabbi Jose said: 'On working days one must cut out the Divine Names that are contained in the text, hide them and burn the rest'. Rabbi Tarfon said: 'May I bury my son if I don't burn them together with the Divine Names that they contain if I come across them". -From the English translation of Dr. H.Freedman.

The word "Minim" means "sectarians" and according to Dr. Freedman it's very probable that in this passage it indicates the Jewish-Christians. The expression "the white spaces" translates the original "gilyohnim" and could have meant, using the word ironically, that the writings of the "Minim where as worthy as a blank scroll, namely nothing. In some dictionaries this word is given as "Gospels". In harmony with this, the sentence that appears in the Talmud before the above mentioned passage says: "The books of the Minim are like white spaces (gilyohnim)."

So in the book Who was a Jew?, of L.H.Schiffman, the above mentioned passage of the Talmud is translated: "We don't save the Gospels or the books of Minim from the fire. They are burnt where they are, together with their Tetragrammatons. Rabbi Yose Ha-Gelili says: "During the week one should take the Tetragrammatons from them, hide them and burn the rest". Rabbi Tarfon said: 'May I bury my children! If I would have them in my hands, I would burn them with all their Tetragrammatons'". Dr. Schiffman continues reasoning that here "Minim" is referred to Hebrew Christians.

And it's very probable that here the Talmud refers to the Hebrew Christians. It is a supposition that finds agreement among the studious people, and in the Talmud seems to be well supported by the context. In Shabbath the passage that follows the above mentioned quotations relates a story, regarding Gamaliel and Christian judge in which there is an allusion to parts of the Sermon on the Mount. Therefore, this passage of the Talmud is a clear indication that the Christians included the Tetragrammaton in their Gospel and their writings.

Because of all we have said there are valid reasons to assert that the writers of the New Testament reported the Tetragrammaton in their divinely inspired work.

Matteo Pierro Salita S. Giovanni 5, 84135 Salerno, ITALY. e-mail cdb@supereva.it 

Friday 14 May 2021

On the divine name in ancient copies of the Greek Septuagint.

 

Historic discovery’ of ancient Biblical fragments made in Israel

Archaeologists have unearthed fragments of a 1,900-year-old Biblical scroll in Israel, in what experts are calling the most important discovery in the last 60 years.

By Devin Watkins

The Israel Antiquities Authority (IAA) has unveiled an historic discovery of Biblical proportions in several desert caves.

In a dig that began in 2017, archaeologists discovered around 80 new parchment fragments of Old Testament texts.

They contain verses written in Greek—with the name of God appearing in Hebrew—from the books of Zechariah and Nahum, which are part of the Book of the Twelve Minor Prophets.

The fragments form part of a scroll which experts believe belonged to Jewish rebels, led by Simon Bar Kokhba, who hid in the caves after a failed revolt against Roman rule between 132 and 136 AD.

Israeli archaeologists began the operation in the Judean desert to prevent caves from being looted. They also unearthed a cache of rare coins from the same period, a 6,000-year-old skeleton of a child, and a large woven basket dating from around 10,500 years ago, the oldest intact in the world. Read article Here

Monday 10 May 2021

File under" Well said." LXXIII

 

"Without education, we are in a horrible and deadly danger of taking educated people seriously."
G.K. Chesterton