The Watchtower Society's commentary on biblical manuscripts

MANUSCRIPTS OF THE BIBLE:

The Holy Scriptures have a superhuman origin as to content but a human history as to their writing and preservation. Moses began compiling them under divine inspiration in 1513 B.C.E., and the apostle John wrote the final portion thereof more than 1,600 years later. The Bible was not originally one book, but as time passed, a demand arose for copies of its various books. This was so, for instance, after the Babylonian exile, for not all released Jews returned to the land of Judah. Instead, many settled elsewhere, and synagogues sprang up throughout the vast territory of the resultant Jewish Dispersion. Scribes prepared copies of the Scriptures needed for these synagogues where the Jews gathered to hear the reading of God’s Word. (Ac 15:21) In later times, among Christ’s followers, conscientious copyists labored to reproduce the inspired writings for the benefit of the multiplying Christian congregations so that there might be an interchange and general circulation of these.—Col 4:16.

Before printing from movable type became common (from the 15th century C.E. onward), the original Bible writings and also copies of them were handwritten. Hence, they are called manuscripts (Latin, manu scriptus, “written by hand”). A Bible manuscript is a handwritten copy of the Scriptures, the whole or in part, as distinguished from one that is printed. Bible manuscripts were produced principally in the form of rolls and codices.

Materials. There are leather, papyrus, and vellum manuscripts of the Scriptures. The noted Dead Sea Scroll of Isaiah, for instance, is a leather roll. Papyrus, a type of paper made from the fibers of a water plant, was used for Bible manuscripts in the original languages and for translations thereof until about the fourth century C.E. At that time its use for Bible manuscripts began to be superseded by the use of vellum, a fine grade of parchment generally made from calf, lamb, or goat skins, a further development of the earlier use of animal skins as writing material. Such manuscripts as the renowned Codex Sinaiticus (Sinaitic Manuscript) and the Codex Vaticanus (Vatican Manuscript No. 1209) of the fourth century C.E. are parchment, or vellum, codices.

A palimpsest (Lat., palimpsestus; Gr., pa·limʹpse·stos, meaning “scraped again”) is a manuscript from which earlier writing was removed or scraped off to make room for later writing. A noted Bible palimpsest is the Codex Ephraemi Syri rescriptus of the fifth century C.E. If the earlier writing (the writing scraped off) is the important one on the palimpsest, scholars can often read this erased writing by employing technical means that include the use of chemical reagents and photography. Some manuscripts of the Christian Greek Scriptures are lectionaries, selected Bible readings for use at religious services.

Styles of Writing. Bible manuscripts written in Greek (whether translations of the Hebrew Scriptures, or copies of the Christian Greek Scriptures, or both) can be divided, or classified, as to writing style, which is also an aid in dating them. The older style (employed especially down to the ninth century C.E.) is the uncial manuscript, written in large, separated capital letters. In it there is generally no word separation, and punctuation and accent marks are lacking. The Codex Sinaiticus is such an uncial manuscript. Changes in writing style began to develop in the sixth century, eventually leading (in the ninth century C.E.) to the cursive, or minuscule, manuscript, written in smaller letters, many of which were joined in a running or flowing writing style. The majority of extant manuscripts of the Christian Greek Scriptures have a cursive script. Cursive manuscripts remained in vogue until the inception of printing.

Copyists. As far as is known today, no handwritten original, or autograph, manuscripts of the Bible are in existence. Yet the Bible has been preserved in accurate, reliable form because Biblical copyists in general, accepting the Scriptures as being divinely inspired, sought perfection in their arduous labor of producing manuscript copies of God’s Word.

The men who copied the Hebrew Scriptures in the days of Jesus Christ’s ministry on earth and for centuries before that time were called scribes (Heb., soh·pherimʹ). Among the early scribes was Ezra, spoken of in the Scriptures as “a skilled copyist.” (Ezr 7:6) Later scribes made some deliberate alterations of the Hebrew text. But their scribal successors, the Masoretes, detected these and recorded them in the Masora, or notes appearing in the margins of the Hebrew Masoretic text they produced.

Copyists of the Christian Greek Scriptures also made earnest efforts to reproduce faithfully the text of the Scriptures.

What assurance is there that the Bible has not been changed?

Despite the care exercised by copyists of Bible manuscripts, a number of small scribal errors and alterations crept into the text. On the whole, these are insignificant and have no bearing on the Bible’s general integrity. They have been detected and corrected by means of careful scholastic collation or critical comparison of the many extant manuscripts and ancient versions. Critical study of the Hebrew text of the Scriptures commenced toward the end of the 18th century. Benjamin Kennicott published at Oxford (in 1776-1780) the readings of over 600 Masoretic Hebrew manuscripts, and the Italian scholar Giambernardo de Rossi published at Parma comparisons of 731 manuscripts in 1784 to 1798. Master texts of the Hebrew Scriptures were also produced by the German scholar Baer and, more recently, by C. D. Ginsburg. Hebrew scholar Rudolf Kittel released in 1906 the first edition of his Biblia Hebraica (The Hebrew Bible), providing therein a textual study through a footnote service, comparing many Hebrew manuscripts of the Masoretic text. The basic text he used was the Ben Chayyim text. But, when the older and superior Ben Asher Masoretic texts became available, Kittel undertook the production of an entirely new third edition, which was completed by his colleagues after his death.

The 7th, 8th, and 9th editions of the Biblia Hebraica (1951-1955) furnished the basic text used to render the Hebrew Scriptures into English in the New World Translation of the Holy Scriptures originally published in 1950-1960. A new edition of the Hebrew text, namely Biblia Hebraica Stuttgartensia, is dated 1977. This edition was used for updating the information presented in the footnotes of the New World Translation published in 1984.

The first printed edition of the Christian Greek Scriptures was that appearing in the Complutensian Polyglott (in Greek and Latin), of 1514-1517. Then in 1516 the Dutch scholar Desiderius Erasmus published his first edition of a master Greek text of the Christian Greek Scriptures. It contained many errors, but an improved text thereof was made available through four succeeding editions from 1519 to 1535. Later, Paris printer and editor Robert Estienne, or Stephanus, issued several editions of the Greek “New Testament,” based principally on Erasmus’ text, but having corrections according to the Complutensian Polyglott and 15 late manuscripts. The third edition of Stephanus’ Greek text (issued in 1550) became, in effect, the “Received Text” (called textus receptus in Latin), which was used for many early English versions, including the King James Version of 1611.

Quite noteworthy in more recent times is the master Greek text prepared by J. J. Griesbach, who availed himself of materials gathered by others but who also gave attention to Biblical quotations made by early writers such as Origen. Further, Griesbach studied the readings of various versions, such as the Armenian, Gothic, and Philoxenian. He viewed extant manuscripts as comprising three families, or recensions, the Byzantine, the Western, and the Alexandrian, giving preference to readings in the latter. Editions of his master Greek text were issued between 1774 and 1806, his principal edition of the entire Greek text being published in 1796-1806. Griesbach’s text was used for Sharpe’s English translation of 1840 and is the Greek text printed in The Emphatic Diaglott, by Benjamin Wilson, in 1864.

A Greek master text of the Christian Greek Scriptures that attained wide acceptance is that produced in 1881 by Cambridge University scholars B. F. Westcott and F. J. A. Hort. It was the product of 28 years of independent labor, though they compared notes regularly. Like Griesbach, they divided manuscripts into families and leaned heavily on what they termed the “neutral text,” which included the renowned Sinaitic Manuscript and the Vatican Manuscript No. 1209, both of the fourth century C.E. While Westcott and Hort viewed matters as quite conclusive when these manuscripts agreed and especially when they were supported by other ancient uncial manuscripts, they were not bound to that position. They took every conceivable factor into consideration in endeavoring to solve problems presented by conflicting texts; and when two readings were of equal weight, that, too, was indicated in their master text. The Westcott and Hort text was the one used principally in translating the Christian Greek Scriptures into English in the New World Translation. However, the New World Bible Translation Committee also consulted other excellent Greek texts, among them Nestle’s Greek text (1948).

Commenting on the history of the text of the Christian Greek Scriptures and the results of modern textual research, Professor Kurt Aland wrote: “It can be determined, on the basis of 40 years of experience and with the results which have come to light in examining . . . manuscripts at 1,200 test places: The text of the New Testament has been excellently transmitted, better than any other writing from ancient times; the possibility that manuscripts might yet be found that would change its text decisively is zero.”—Das Neue Testament—zuverlässig überliefert (The New Testament—Reliably Transmitted), Stuttgart, 1986, pp. 27, 28.

The extant manuscripts of the Christian Scriptures (in Greek and other languages) show textual variations. Variations are to be expected in view of human imperfection and the copying and recopying of manuscripts, especially by many copyists who were not professionals. If certain manuscripts had a common ancestor manuscript, perhaps came from a particular revision of early texts, or were produced in a particular area, they would probably have at least some variations in common, and hence they are said to belong to the same family, or group. On the basis of similarity in such differences, scholars have sought to classify the texts into groups, or families, the number of which has increased with the passing of time, till reference is now made to the Alexandrian, Western, Eastern (Syriac and Caesarean), and the Byzantine texts, represented in various manuscripts or in different readings scattered throughout numerous manuscripts. But despite the variations peculiar to different manuscript families (and the variations within each group), the Scriptures have come down to us in essentially the same form as that of the original inspired writings. The variations of reading are of no consequence as to Bible teachings in general. And scholastic collations have corrected errors of any importance, so that today we enjoy an authentic and reliable text.

Since Westcott and Hort produced their refined Greek text, a number of critical editions of the Christian Greek Scriptures have been produced. Noteworthy among them is The Greek New Testament published by the United Bible Societies and now in its third edition. Identical in wording is the 26th edition of the so-called Nestle-Aland text, published in 1979 in Stuttgart, Germany.—See CHRISTIAN GREEK SCRIPTURES.

Manuscripts of Hebrew Scriptures. There are possibly 6,000 manuscripts of all or portions of the Hebrew Scriptures extant today in various libraries. The vast majority contain the Masoretic text and are of the tenth century C.E. or thereafter. The Masoretes (of the second half of the first millennium C.E.) sought to transmit the Hebrew text faithfully and made no changes in the wording of the text itself. However, to preserve the traditional pronunciation of the vowelless consonantal text, they devised systems of vowel pointing and accenting. Additionally, in their Masora, or marginal notes, they drew attention to textual peculiarities and gave corrected readings they considered necessary. It is the Masoretic text that appears in printed Hebrew Bibles of the present day.

Damaged Hebrew Scripture manuscripts used in Jewish synagogues were replaced by verified copies, and the defaced or damaged manuscripts were stored in a genizah (a synagogue storeroom or repository). Finally, when it was full, the manuscripts were removed and ceremoniously buried. Doubtless many ancient manuscripts perished in that way. But the contents of the synagogue genizah in Old Cairo were spared, probably because it was walled up and forgotten for centuries. Following the rebuilding of the synagogue in 1890 C.E., the manuscripts in its genizah were reexamined, and from there fairly complete Hebrew Scripture manuscripts and fragments (some said to be of the sixth century C.E.) found their way into various libraries.

One of the oldest extant fragments containing Biblical passages is the Nash Papyrus, found in Egypt and preserved at Cambridge, England. Evidently part of an instructional collection, it is of the second or first century B.C.E. and consists of only four fragments of 24 lines of a pre-Masoretic text of the Ten Commandments and some verses of Deuteronomy, chapters 5 and 6.

Since 1947 many Biblical and non-Biblical scrolls have been found in various areas W of the Dead Sea, and these are referred to generally as the Dead Sea Scrolls. Most significant among them are manuscripts discovered in a number of caves in and about the Wadi Qumran (Nahal Qumeran). These are also known as the Qumran texts and evidently once belonged to a Jewish religious community centered at nearby Khirbet Qumran (Horvat Qumeran). The first discovery was made by a Bedouin in a cave about 15 km (9.5 mi) S of Jericho, where he found a number of earthenware jars containing ancient manuscripts. One of these was the now-renowned Dead Sea Scroll of Isaiah (1QIs⁠a), a well-preserved leather roll of the entire book of Isaiah, except for a few gaps. (PICTURE, Vol. 1, p. 322) It contains a pre-Masoretic Hebrew script and has been dated toward the end of the second century B.C.E. Hence, it is about a thousand years older than the oldest extant manuscript of the Masoretic text. However, though showing some differences in spelling and grammatical construction, it does not vary doctrinally from the Masoretic text. Among the documents recovered in the Qumran area are fragments of over 170 scrolls representing parts of all Hebrew Scripture books except Esther, and in the case of some books, more than one copy exists. These manuscript scrolls and fragments are believed to range in date from about 250 B.C.E. to about the middle of the first century C.E., and they exhibit more than one type of Hebrew text, such as a proto-Masoretic text or one underlying the Greek Septuagint. Studies of such materials are still in progress.

Among notable vellum Hebrew manuscripts of the Hebrew Scriptures is the Cairo Karaite Codex of the Prophets. It contains the Masora and vocalization, and its colophon indicates that it was completed in about 895 C.E. by the noted Masorete Moses ben Asher of Tiberias. Another significant manuscript (of 916 C.E.) is the Petersburg Codex of the Latter Prophets. The Aleppo Sephardic Codex, once preserved at Aleppo, Syria, and now in Israel, until recently contained the entire Hebrew Scriptures. Its original consonantal text was corrected, punctuated, and furnished with the Masora about 930 C.E. by Aaron ben Asher, son of Moses ben Asher. The oldest dated manuscript of the complete Hebrew Scriptures in Hebrew is the Leningrad Manuscript No. B 19⁠A, preserved in the Public Library in St. Petersburg, Russia. It was copied in 1008 C.E. “from the corrected books prepared and annotated by Aaron ben Moses ben Asher the teacher.” Another noteworthy Hebrew manuscript is a codex of the Pentateuch preserved in the British Library (Codex Oriental 4445), consisting of Genesis 39:20 to Deuteronomy 1:33 (except for Nu 7:46-73 and 9:12–10:18, which are lacking or have been supplied by a later hand) and probably dating from the tenth century C.E.

Many manuscripts of the Hebrew Scripture portion of the Bible were written in Greek. Among those of particular note is one in the collection of the Fouad Papyri (Inventory Number 266, belonging to the Société Egyptienne de Papyrologie, Cairo), containing portions of Genesis and of the second half of Deuteronomy according to the Septuagint. It is of the first century B.C.E. and shows, in various places, the divine name written in square Hebrew characters within the Greek text. Fragments of Deuteronomy, chapters 23 to 28, are found in Rylands Papyrus iii. 458 of the second century B.C.E., preserved in Manchester, England. Another leading manuscript of the Septuagint contains fragments of Jonah, Micah, Habakkuk, Zephaniah, and Zechariah. In this leather scroll, dated to the end of the first century C.E., the divine name is rendered by the Tetragrammaton written in ancient Hebrew characters.—See NW appendix, pp. 1562-1564.

Manuscripts of Christian Greek Scriptures. The Christian Scriptures were written in Koine. Though no original autograph manuscripts thereof are known to exist today, according to one calculation, there are some 5,000 extant manuscript copies, whole or in part, of these Scriptures in Greek.

Papyrus manuscripts. Biblical papyri of great importance were among papyrus codices found in Egypt about 1930, their purchase being announced in 1931. Some of these Greek codices (dating from the second to the fourth centuries C.E.) consist of parts of eight Hebrew Scripture books (Genesis, Numbers, Deuteronomy, Isaiah, Jeremiah, Ezekiel, Daniel, and Esther), and three contain portions of 15 books of the Christian Greek Scriptures. Most of these Scriptural papyri were purchased by an American manuscript collector, A. Chester Beatty, and are now preserved in Dublin, Ireland. The rest were acquired by the University of Michigan and by others.

The international designation for Biblical papyri is a capital “P” followed by a small superior number. The Chester Beatty Papyrus No. 1 (P⁠45) consists of parts of 30 leaves from a codex that probably once had about 220 leaves. P⁠45 has portions of the four Gospels and the book of Acts. The Chester Beatty Papyrus No. 3 (P⁠47) is a fragmentary codex of Revelation containing ten somewhat damaged leaves. These two papyri are believed to be from the third century C.E. Quite noteworthy is the Chester Beatty Papyrus No. 2 (P⁠46) believed to be from about 200 C.E. It has 86 somewhat damaged leaves out of a codex that probably had 104 leaves originally, and it still contains nine of Paul’s inspired letters: Romans, Hebrews, First Corinthians, Second Corinthians, Ephesians, Galatians, Philippians, Colossians, and First Thessalonians. It is noteworthy that the letter to the Hebrews is included in this early codex. Since Hebrews does not give its writer’s name, its composition by Paul has frequently been disputed. But this letter’s inclusion in P⁠46, evidently consisting of Paul’s letters exclusively, indicates that in about 200 C.E., Hebrews was accepted by early Christians as an inspired writing of the apostle Paul. The letter to the Ephesians appears in this codex, thus also refuting arguments that Paul did not write this letter.

At the John Rylands Library, Manchester, England, there is a small papyrus fragment of John’s Gospel (some verses of chapter 18) cataloged as Rylands Papyrus 457. It is internationally designated as P⁠52. This is the oldest extant manuscript fragment of the Christian Greek Scriptures, having been written in the first half of the second century, possibly about 125 C.E., and thus only a quarter of a century or so after John’s death. The fact that a copy of John’s Gospel was evidently circulating in Egypt (the place of the fragment’s discovery) by that time shows that the good news according to John was really recorded in the first century C.E. and by John himself, not by some unknown writer well along in the second century C.E., after John’s death, as some critics once claimed.

The most important addition to the collection of Biblical papyri since the discovery of the Chester Beatty Papyri was the acquisition of the Bodmer Papyri, published between 1956 and 1961. Particularly noteworthy are Papyrus Bodmer 2 (P⁠66) and Papyrus Bodmer 14, 15 (P⁠75), both written about 200 C.E. Papyrus Bodmer 2 contains a large part of the Gospel of John, while Papyrus Bodmer 14, 15 has much of Luke and John and is textually very close to Vatican Manuscript No. 1209.

Vellum manuscripts. Bible manuscripts written on vellum sometimes include both the Hebrew and Christian Greek Scripture portions of the Bible, though some are only of the Christian Scriptures.

Codex Bezae, designated by the letter “D,” is a valuable manuscript of the fifth century C.E. Though its actual place of origin is unknown, it was acquired in France in 1562. It contains the Gospels, the book of Acts, and only a few other verses, and is an uncial manuscript, written in Greek on the left-hand pages, with a parallel Latin text appearing on the right-hand pages. This codex is preserved at Cambridge University in England, having been presented to that institution by Theodore Beza in 1581.

Codex Claromontanus (D2) is likewise written in Greek and Latin on opposite pages, Greek on the left and Latin on the right. It contains Paul’s canonical letters, including Hebrews, and is considered to be of the sixth century. It was reportedly found in the monastery at Clermont, France, and was acquired by Theodore Beza, but it is now preserved at the Bibliothèque Nationale in Paris.

Among more recently discovered vellum manuscripts of the Christian Greek Scriptures is Codex Washingtonianus I, containing the Gospels in Greek (in the common Western order: Matthew, John, Luke, and Mark). It was obtained in 1906 in Egypt and is preserved at the Freer Gallery of Art, Washington, D.C. The international symbol of this codex is “W,” and it is thought to have been written in the fifth century C.E., except that apparently, because of damage, part of John was replaced in the seventh century C.E. Codex Washingtonianus II, having the symbol “I,” is also in the Freer Collection and contains portions of Paul’s canonical letters, including Hebrews. This codex is believed to have been written in the fifth century C.E.

Hebrew and Christian Greek Scriptures. The most important and most complete extant Bible manuscripts in Greek were written on vellum in uncial letters.

Vatican Manuscript No. 1209. The Vatican Manuscript No. 1209 (Codex Vaticanus), designated internationally by the symbol “B,” is an uncial codex of the fourth century C.E., possibly produced in Alexandria, and it originally contained the entire Bible in Greek. A corrector of later date retraced the letters, perhaps because the original writing had faded, except that he skipped letters and words he considered incorrect. Originally this codex probably had approximately 820 leaves, of which 759 remain. Most of Genesis is gone, as well as a part of Psalms, Hebrews 9:14 to 13:25, and all of First and Second Timothy, Titus, Philemon, and Revelation. Codex Vaticanus is preserved at the Vatican Library in Rome, Italy, and is known to have been there as early as the 15th century. However, Vatican Library authorities made access to the manuscript extremely difficult for scholars and did not publish a full photographic facsimile of the entire codex until 1889-1890.

Sinaitic Manuscript. The Sinaitic Manuscript (Codex Sinaiticus) is also of the fourth century C.E., but Codex Vaticanus may be a little older. The Sinaitic Manuscript is designated by the symbol א (ʼaʹleph, first letter in the Hebrew alphabet), and while it evidently once contained the entire Bible in Greek, part of the Hebrew Scriptures has been lost. However, it has all the Christian Greek Scriptures. Likely this codex originally consisted of 730 leaves, at least, though the whole or parts of just 393 are now verified to be extant. It was discovered (one portion in 1844 and another in 1859) by the Bible scholar Konstantin von Tischendorf at the Monastery of St. Catherine at Mount Sinai. Forty-three leaves of this codex are kept in Leipzig, portions of three leaves are at St. Petersburg, Russia, and 347 leaves are preserved at the British Library in London. It has been reported that 8 to 14 more leaves were discovered in the same monastery in 1975.

Alexandrine Manuscript. The Alexandrine Manuscript (Codex Alexandrinus), designated by the letter “A,” is a Greek uncial manuscript containing most of the Bible, including the book of Revelation. Of possibly 820 original leaves, 773 have been preserved. This codex is generally considered to be of the first half of the fifth century C.E., and it is also preserved in the British Library.—PICTURE, Vol. 2, p. 336.

Codex Ephraemi Syri rescriptus. The Codex Ephraemi Syri rescriptus (Codex Ephraemi), designated internationally by the letter “C,” is also generally considered to have originated in the fifth century C.E. It is written in Greek uncials on vellum and is a rewritten codex, a palimpsest manuscript. The original Greek text was removed, and a number of leaves were then written over with discourses of Ephraem Syrus (the Syrian), rendered in Greek. This was done probably during the 12th century, when there was a scarcity of vellum. However, the underlying text has been deciphered. While “C” evidently once contained all the Scriptures in Greek, just 209 leaves remain, 145 being of the Christian Greek Scriptures. Hence, this codex now contains only portions of Hebrew Scripture books and parts of all books of the Christian Greek Scriptures except Second Thessalonians and Second John. It is preserved at the Bibliothèque Nationale in Paris.

Reliability of the Bible Text. Appreciation of the reliability of the Bible is greatly enhanced when it is realized that, by comparison, there are only very few extant manuscripts of the works of classical secular writers and none of these are original, autograph manuscripts. Though they are only copies made centuries after the death of the authors, present-day scholars accept such late copies as sufficient evidence of the authenticity of the text.

Extant Hebrew manuscripts of the Scriptures were prepared with great care. Respecting the text of the Hebrew Scriptures, scholar W. H. Green observed: “It may be safely said that no other work of antiquity has been so accurately transmitted.” (Archaeology and Bible History, by J. P. Free, 1964, p. 5) The late Bible text scholar Sir Frederic Kenyon made this reassuring statement in the introduction to his seven volumes entitled The Chester Beatty Biblical Papyri: “The first and most important conclusion derived from the examination of them [the Papyri] is the satisfactory one that they confirm the essential soundness of the existing texts. No striking or fundamental variation is shown either in the Old or the New Testament. There are no important omissions or additions of passages, and no variations which affect vital facts or doctrines. The variations of text affect minor matters, such as the order of words or the precise words used. . . . But their essential importance is their confirmation, by evidence of an earlier date than was hitherto available, of the integrity of our existing texts. In this respect they are an acquisition of epoch-making value.”—London, 1933, Fasciculus I, p. 15.

Concerning the Christian Greek Scriptures, Sir Frederic Kenyon stated: “The interval then between the dates of original composition and the earliest extant evidence becomes so small as to be in fact negligible, and the last foundation for any doubt that the Scriptures have come down to us substantially as they were written has now been removed. Both the authenticity and the general integrity of the books of the New Testament may be regarded as finally established.”—The Bible and Archæology, 1940, pp. 288, 289.


Centuries ago, Jesus Christ, “the faithful and true witness” (Re 3:14), repeatedly and emphatically confirmed the genuineness of the Hebrew Scriptures, as did his apostles. (Lu 24:27, 44; Ro 15:4) Extant ancient versions, or translations, further bespeak the exactness of the preserved Hebrew Scriptures. Manuscripts and versions of the Christian Greek Scriptures bear unassailable testimony to the marvelous preservation and accurate transmission of that portion of God’s Word. We are therefore now favored with an authentic, thoroughly reliable Bible text. A thoughtful examination of preserved manuscripts of the Holy Scriptures bears eloquent testimony to their faithful preservation and permanence, giving added meaning to the inspired statement: “The green grass has dried up, the blossom has withered; but as for the word of our God, it will last to time indefinite.”—Isa 40:8; 1Pe 1:24, 25.

Exaptation:Darwinian code for spin?

Darwinism's tree of life examined

It's Design all the way down VIII

It's design all the way down VII

UT Southwestern physiologists uncover a new code at the heart of biology
UT SOUTHWESTERN MEDICAL CENTER

DALLAS - Sept. 23, 2015 - UT Southwestern physiologists trying to understand the genetic code have found a previously unknown code that helps explain which protein should be created to form a particular type of cell.

The human body is made up of tens of trillions of cells. Each cell contains thousands of proteins, which determine how the cell should form and what functions it needs to perform. Proteins, in turn, are made up of hundreds of amino acids. The blueprint for each protein is specified by genetic codons, which are triplets of nucleotides that can make 20 different types of amino acids. The way in which amino acids are linked together then determines which proteins are eventually produced, and in turn, what functions the cell will have.

What researchers found was that not only does the sequence of the amino acids matter, but so does the speed of the process in which the amino acids are put together into a functional protein.

"Our results uncovered a new 'code' within the genetic code. We feel this is quite important, as the finding uncovers an important regulatory process that impacts all biology," said Dr. Yi Liu, Professor of Physiology.

It was long known that almost every amino acid can be encoded by multiple synonymous codons and that every organism, from humans to fungi, has a preference for certain codons. The researchers found that more frequently used codons ? the "preferred codons" ? speed up the process of producing an amino acid chain, while less frequently produced codons slow the process. The use of either preferred or non-preferred codons is like having speed signs on the protein production highway: some segments need to be made fast and others slow.

 "The genetic code of nucleic acids is central to life, as it specifies the amino acid sequences of proteins," said Dr. Liu, the Louise W. Kahn Scholar in Biomedical Research. "By influencing the speed with which a protein is assembled from amino acid building blocks, the use of "fast" and "slow" codons can affect protein folding, which is the process that allows a protein to form the right shape to perform a specific function. This speed control mechanism makes sure that proteins are assembled and folded properly in different cells. Therefore, the genetic code not only specifies the sequence of amino acids but also the shape of the protein."

The researchers found that proteins with identical amino acid sequences can have different functions if they are assembled at different speeds. This can have important implications for identifying human disease-causing mutations because this study indicates that a mutation does not have to change amino acid identity to cause a disease. In fact, most mutations in human DNA do not result in amino acid change.

"Therefore, our study indicates that the new "code" ? the speed limit of assembly ? within the genetic code can dictate the ultimate function of a given protein," said Dr. Liu.

The findings appear as the cover story of the journal Molecular Cell, one of the top molecular biology, biophysics, and biochemistry journals.

The latest findings extend prior research published by Dr. Liu and colleagues in Nature in 2013 that broke new ground by demonstrating that synonymous codons of a circadian clock protein are not the same in making functional proteins, despite the fact that they encode the same amino acids.  Genes can adapt to different environmental changes by choosing the most optimal codon, which is counterintuitive to natural selection.

Dr. Liu and his team are able to study these systems using a type of bread mold fungus called Neurospora crassa. The use of the mold allows for easy manipulation of its genes and codons in the laboratory that are more difficult to do in animals. Dr. Liu's lab is also trying to unravel the secrets of chronobiology and the molecular mechanisms that underlie an organism's daily biological clock, called the circadian clock. Biological clocks have been described in almost all organisms ranging in complexity from single cell organisms to mammals, and to function in the control of daily rhythms such as sleep-wake and activity cycles, body temperature cycles, endocrine functions, and gene expression.

###

Other UT Southwestern researchers involved include postdoctoral researchers Chien-Hung Yu, Yunkun Dang, Zhipeng Zhou, first co-authors, and graduate student researcher Fangzhou Zhao. They collaborated with the lab of Dr. Matthew Sachs, Professor of Biology at Texas A&M University.

The work is supported by grants from the National Institutes of Health and the Welch Foundation.

About UT Southwestern Medical Center


UT Southwestern, one of the premier academic medical centers in the nation, integrates pioneering biomedical research with exceptional clinical care and education. The institution's faculty includes many distinguished members, including six who have been awarded Nobel Prizes since 1985. The faculty of more than 2,700 is responsible for groundbreaking medical advances and is committed to translating science-driven research quickly to new clinical treatments. UT Southwestern physicians provide medical care in 40 specialties to about 92,000 hospitalized patients and oversee approximately 2.1 million outpatient visits a year.

On the Hubris of Scientism?

Human Cloning Advance: Ban Now or Cry Later
Wesley J. Smith November 1, 2015 4:45 AM 


Human cloning used to make big headlines. But "the scientists" got smart, and just started using the scientific term for cloning -- somatic cell nuclear transfer -- as a way of hiding in plain sight.

Thus, when the first human embryos were successfully manufactured via SCNT, the were few headlines and most people yawned -- if they heard about it at all. Of course, I reacted strongly.

Now, the South Koreans have improved the efficiency of cloning, and again, the scientists are keeping mostly mum in the popular media so as to not alert us rubes that Brave New World is approaching. From the KBS World News Radio story:

A group of medical experts has succeeded at improving the efficiency of human somatic cell nuclear transfer (SCNT) by three times.

A research team at Cha Medical Group said Friday that it found ways to enhance the efficiency of SCNT by discovering a correlation between the quality of female eggs and the success rate of SCNT embryo development.,,

The team said it has made five pilot medicine products using the new findings and plans to seek the government's approval for a large-sized clinical test by the end of this year.


Now, add in the jet-speed advance in genetic engineering known as CRSPR. We are coming closer to the day of manufacturing human beings via cloning, genetically engineered for desired traits.

On non-verbal communication

On those still in chains

On pitching a design inference to a hostile audience.

For SETI Researchers, Here Is a Guide for Handling Fallacious Objections
Casey Luskin October 30, 2015 11:08 AM


A recent story making the rounds, "Space anomaly gets extraterrestrial intelligence experts' attention," claims that the Search for Extra Terrestrial Intelligence (SETI) project has found "a strange star" that "could mean alien life." As David Klinghoffer noted in an earlier post, the raw data entails odd fluctuations in the intensity of light coming from a star. CNN reports:

The Search for Extraterrestrial Intelligence Institute has its eyes -- and soon possibly one of the United States' premier telescopes -- focused on an anomaly that some astronomers can't quite explain.
[...]

"What was unusual about that was the depth of the light dips, up to 20% decrease in light, and the timescales (of light variation) -- a week to a couple of months."

So what's the explanation? Could it be from a swarm of comets? Some sort of intergalactic phenomenon that Earthbound scientists haven't discovered? Or an effect of planet-sized structures built by some sort of alien civilization?

Comparisons between SETI's methodology and the theory of intelligent design (ID) have been made since ID's earliest days. Both SETI and ID seek to detect the signs of intelligence in the world around us. SETI focuses on looking for evidence of extraterrestrial civilizations far away in the universe. ID looks for signs of intelligent agency in the origin of living organisms and the universe itself.
SETI and ID share something else: they both try to be very conservative and cautious, invoking intelligent causation only when it is clearly warranted by the evidence. Here's how one SETI scientist handles this:

Jason Wright, a Penn State astronomy professor, saw Boyajian's data and can't quite explain it. But in a post Thursday to his website, he cautioned against jumping to conclusions -- as some apparently have -- that intelligent beings far away are behind this oddity.
"My philosophy of SETI," Wright wrote, referring to the search for extraterrestrial intelligence, "is that you should reserve your alien hypothesis as a last resort." He also cited "Cochran's Commandment to planet hunters ... Thou shalt not embarrass thyself and they colleagues by claiming false planets.

That's a good philosophy, and ID takes a similar approach. ID proponents only conclude in favor of design when it's clear that known material causes cannot explain the observed phenomena and when the data is best explained by intelligence.
So far, SETI hasn't found a case that is clearly explained by some extraterrestrial civilization. This recent find of a star with flickering light is nowhere near enough evidence to conclude that aliens are the best explanation -- in fact Tech Insider reports that the data could be explained by a "lopsided star" wherein its irregular shape "creates patches of darker and lighter regions within these kinds of stars, so the light curves that make it back to Earth won't look completely uniform."

But suppose SETI were to one day discover strong evidence of some extraterrestrial civilization -- enough to warrant a design inference. They might expect to face some of the same fallacious objections that ID faces. They might like some friendly tips on handling them. Here's a little guide for SETI folks if that day ever comes:

Who Made the Aliens?

As soon as you claim you've detected aliens, skeptics will say "How can you claim there are aliens when you haven't explained who made the aliens?"

The answer to this is very simple: We don't need to be able to explain the origin of the aliens to recognize evidence of them. For example, let's say that Chewbacca, Spock, and ET were standing right in front of you. Would you say to them, "Look, I'm not going to believe any of you actually exist until you tell me where you came from"?

(I should add that it could be very fair to ask where the aliens came from because in an ultimate sense they require an explanation -- but it's not a fair question to ask if your only purpose is to question whether those aliens exist.)

Where's Your "Alien-O'Meter"?

Some critics might reply "You need some kind of an 'alien-o-meter' to show that these aliens really exist before you can claim that you've detected evidence of an extraterrestrial civilization. After all, how do we know that aliens were behind the evidence you've discovered if we don't know the aliens exist?"

The answer to this one is a bit more complicated. But a little explanation shows this objection to be nonsensical and based upon a complete misunderstanding of how we make scientific inferences.

Some ID critics mistakenly think you have to directly witness the designer in action with your own eyes in order to detect design. Sometimes misguided creationists make an analogous critique of evolution, saying that you can never infer evolution if no one was around to see it. Both groups misunderstand the nature of historical sciences.

Historical sciences operate under the principle of uniformitarianism, which assumes that the way the natural world works today is similar to how it worked in the past. In other words, "the present is the key to the past." If we see certain causes at work in the world as we know it and we learn to recognize their known effects, then when we find those same effects in the historical record, we can infer that the same causes were at work. As I have explained before:

Recently an atheist student emailed me to ask how it's reasonable to claim that an "unobserved designer" is responsible for complex features of nature, like high CSI (complex specified information) and irreducibly complex structures. In reply, I explained that first we must ask the question "What does it mean to 'observe' or 'detect' something?" Here's a start:
Our eyes can help us observe objects in nature by seeing light reflected from those objects.
Our ears can help us detect objects in nature by receiving sound emitted from them.
Our nose can help us detect objects in nature by receiving emitted chemicals which we register as a "smell."
Our skin can help us detect objects in nature by receiving signals that tell us about shape, texture, and even temperature.
So when we see a campfire, how do we "observe" it? Our sense organs receive patterns of light, sound, smell, and heat, which our brains recognize and match to fires we've seen in the past. Our brain thinks, in effect, "Okay, as in the past, when the eyes receive a particular pattern of yellow and red light, the ears hear a crackling sound, the nose receives the smell of smoke, and the skin feels heat, that's a campfire." So we recognize and observe something by receiving a pattern of information through our sense organs and then matching it to a pattern we've seen in the past.
Our senses also make another set of observations about a campfire: the morning after a campfire, we observe that there's a bunch of blackened and charred wood, ash and soot, and smoke rising from within a circle of blackened stones. We smell the smoke and ash, and it might be slightly warm from remaining embers from the night before.

So let's say now that we're taking a morning stroll and come upon a circle of blackened stones, charred wood, ash, and soot. There's a little smoke rising from the center, and it's slightly warm. We didn't see a fire directly with our eyes. But our senses tell us that there is evidence that a fire was there. In this case, the most reasonable inference to make is that there was a campfire, even though we can't directly observe it.

Thus, just because something is "unobservable" by our eyes at this exact moment, doesn't mean we can't find compelling evidence that it exists, or that it was present. We must not toss out the word "unobservable" as if it somehow blocks the design inference. We regularly make inferences to unobserved objects and events (like a campfire) by using our senses to detect evidence that reliably indicates that a particular object or event was present (like finding a circle of blackened stones, charred wood, soot, and smoke).

We can use exactly the same method of reasoning to detect design at the heart of biology. In all of our experience, high CSI and irreducible complexity ONLY come from intelligent agents. Thus, based upon our experience of the cause-and-effect structure of the world we observe around us, we are justified in inferring that a mind was at work. ...[W]hen we find high CSI entities like language-based digital codes or irreducibly complex molecular machines, we are justified in inferring that an intelligent agent was at work. Why? Because, in our experience, these things always trace back to a mind. We might not directly see that mind, but we can infer that a mind was present to create the known observed effects.

This is the positive argument for intelligent design, and it is just like inferring that a campfire was present based on remaining physical evidence. One need not directly see the fire, or know who tended it, or why he or she or they did so, to draw a reasonable inference that a fire was present.

So to the critic who asks "Where's the alien-o-meter," SETI's response might go like this: We have an alien-o-meter, but it's not what you think it is. We don't need to Skype with ET to potentially know he's there. If we find in space the kind of evidence that, in our experience, only comes from intelligent beings, then we can infer that ETs exist.
Aliens of the Gaps

A last objection the SETI researcher will face goes like this: You're never allowed to conclude that aliens are responsible for anything because someday we might find a fully material, physical explanation other than ETs for the evidence you claim demonstrates an extraterrestrial civilization. As materialist explanations advance, your "alien" theory will just retreat into the gaps of our knowledge.

Now this objection might have a little more traction than the others. Nobody wants to invoke intelligent aliens only to have them later explained away by some unintelligent material cause. As SETI proponent Jason Wright said, it should be a "last resort." And indeed, in this case that's a good philosophy since the "lopsided star" theory seems to explain the observed data quite well.

But does the fact that some cases aren't best explained by intelligence that mean you can never invoke intelligent causes? Of course not! It just means one needs to be careful and cautious about invoking intelligent design.

What the gaps fallacy really says is, "While your explanation may seem correct today, new evidence may be revealed tomorrow to provide a material explanation and show that intelligent causes aren't the best explanation." That's a fair point, but the reality is that every type of explanation -- material or intelligent -- is subject to the same problem.

Indeed, any explanation could be subject to the "gaps" charge. This is a problem that every kind of explanation in science potentially faces. That's why scientific explanations are always held tentatively and never asserted with complete finality or absolute certainty. Scientific explanations are always subject to revision if newly uncovered data shows they are wrong. This is true whether we're dealing with Darwinian evolution or intelligent design, aliens or standard stellar dynamics.

So at the end of the day, what the "gaps" objection really ought to say is "Today X is the best explanation, but let's hold it tentatively." Nothing wrong with that -- that's how all science ought to work.

What the gaps charge often indicates is that some kind of explanation is assumed to be the default, privileged answer, and that we can only deviate from that default answer under extraordinary circumstances. In the case of intelligent design or SETI, it's material causes that are being privileged. Many who make the "gaps" charge want material causes to have an absolute privilege that precludes making a design inference in all circumstances. But given that we can detect intelligent causation, why should material causes enjoy such an absolute privilege?

Unless we are to privilege material causes on principle and deny our ability to ever infer intelligent causes, the gaps objection fails. But since we know what intelligent causes can do, and because we can reliably detect the prior action of intelligent agents, we can't say that in all cases it's wrong to detect design. We can detect design, and so long as we hold the conclusion of design tentatively, the gaps objection isn't fatal.

Don't Miss the Irony

Now I personally don't object to SETI researchers doing their thing, but I'm highly skeptical that they're ever going to find an extraterrestrial civilization. But my reason for writing this isn't to rant against SETI. It's just to point out the irony. People make a lot of fallacious objections against intelligent causation. We in the ID movement get this all the time. It sounds like, "Who designed the designer?" or "Where's your theo-meter?" or "This is just God of the gaps." If SETI claimed to find some extraterrestrial intelligent civilization, most likely the analagous objections would never come up, at least not with much force.

Why is that? Most materialists would see extraterrestrial life as proof that a naturalistic origin of life is possible, and that perhaps life is therefore common in our universe. After all, what drives many materialists to look for evidence of extraterrestrial life is a misguided assumption that if aliens exist, it would somehow validates their worldview.


But they are mistaken about what SETI means. If we found evidence of an alien civilization, that wouldn't be evidence that life evolves naturally. It would just be evidence for an extraterrestrial civilization. That's it. How it arose would be an entirely different question. And all indications we have so far show that life could not arise naturally, whether on earth or anywhere else. For all we know, finding evidence of extraterrestrial life could end up being yet another piece of evidence pointing to intelligent design.

Yet more realism about the Cambrian explosion from Darwinists

The Economist Admits Cambrian Explosion Is a "Mystery"

Casey Luskin October 29, 2015 11:12 AM 

A recent video from The Economist takes on the evolution of animals in the Cambrian explosion, conceding something that many Darwin advocates refuse to fully acknowledge: that "biology's big bang" is a "mystery." Find it here. Among other important admissions, it says:

• Narrator: "The cause of this sudden burst of life, which geologists call the Cambrian explosion, remains a mystery."


• Andrew Parker, Professor of Life Sciences at the Natural History Museum of London: "The Cambrian explosion was really biology's big bang. Things went from moving really slowly on the sea floor without any predation to suddenly all the different type of ecologies that we see today. Life literally exploded."


• Simon Conway Morris, Professor of Evolutionary Paleobiology at the University of Cambridge: "What triggered the Cambrian explosion? We don't really know. There are many different possibilities, different hypotheses. And we've got to remember that cause and effect are often difficult to disentangle."

The video then discusses the period prior to the Cambrian called the Ediacaran. But Conway Morris admits that the organisms that lived in this period are not clearly related to the Cambrian animals: "Before the Cambrian we go into what's called the Ediacaran times. And this is an extraordinary interval where we have the sea floor populated by basically weird creatures. And quite frankly we're not quite sure if they're animals or something else entirely." He explains that these strange organisms "seem to more or less disappear as the Cambrian explosion kicks off."

This is a nice statement of the problem. The video offers some of the standard weak and inadequate explanations we've seen in the past for how the Cambrian explosion occurred. For example, it cites rising oxygen levels as a possible trigger for building larger animals. We have discussed the problems with that theory here, here, here, and here. The video admits, "Evidence to support this theory of higher oxygen levels is scarce" since the ice ages that might have led to larger algae populations which raised oxygen levels "ended 90 million years before the Cambrian." Indeed, Simon Conway Morris casts doubt on this theory by acknowledging that "oxygen was increasing already, much, much before" the Cambrian period.

The video also notes the hypothesis "that minerals became increasingly available in the oceans due to post-glacial erosion." These minerals might have spurred the evolution of shells, but the video notes a problem with this hypothesis:

But Cambrian shells were made from a range of materials. This suggests they [were] the result of parallel evolution in different animals lines, not a single innovation. That means something encouraged them to develop on more than one occasion. And shells are costly to make. It's unlikely mere abundance of minerals would have been enough.

We've discussed problems with this hypothesis here and here.

So how did the Cambrian animals evolve so rapidly? The key to understanding the typical evolutionary position on this question is to appreciate that most evolutionists really aren't trying to answer that question -- at least not in any meaningful way.

ID proponents look at the question and think, "Well, to build all these animals you're going to need an extraordinary amount of new genetic and epigenetic information, and it's got to arise very quickly. We must identify some mechanism -- evolutionary or otherwise -- that can accomplish this feat."

Evolutionary scientists look at the same question and usually assume that all the information could arise whenever it's needed. They're just looking for some kind of trigger to create a selectable need for complex biological systems, and voila, everything happens. They assume that the information needed to build the Cambrian animals already existed prior to the Cambrian explosion. For example, consider what Shuhai Xiao, a professor of geobiology at Virginia Tech university, says in the video:

The Cambrian explosion happens after a series of events, in my opinion. First you have genetic building blocks to build an animal. You also need oxygen to support metabolism. But that alone is not sufficient. You also need a mechanism to drive the system into a runaway situation. You need to make the system work very fast. And one of the mechanisms to drive the system to a runaway situation is ecological feedback.

Notice that Xiao simply assumes the existence of a full-fledged animal with all of the requisite "genetic building blocks" from the start. Then, all you need is oxygen and the right ecological conditions and all major animal diversity arises. It seems so easy! But they never even attempt to tackle the origin of new biological information.

Simon Conway Morris takes the same approach:

We're inventing nervous systems. We're inventing eyes and other sensor systems. We're learning how to move fast, how to swim effectively. So you have a whole cascade of feedbacks. And it's really trying to pinpoint "the trigger" versus all the other consequences that flowed from that point.

In other words, explaining the Cambrian explosion entails assuming that a cascade of feedbacks can produce all animal body plans. You just have to look for that one "trigger" that set off the cascade and the rest takes care of itself. But where is the explanation for the origin of all the biological information needed to build these animals? They never touch that question.

An analogy that comes to mind is one we've used before -- the famous Monty Python skit "How to Do It":n the skit, they explain how to cure the diseases of the world, but only in the vaguest and most superficial terms. They never actually give enough information to explain how to "do it" in the real world. The absurdity, of course, is what makes it funny.

The video from The Economist bears a resemblance that's not as funny. Andrew Parker, for example, says that perhaps "vision was actually the only thing that was required to trigger the Cambrian explosion." The Monty Python version might go like this:Question: What's the evolutionary explanation for the origin of all the complex animals that appeared suddenly in the Cambrian explosion?Answer: Well, you see, you start with a full-fledged animal and then it evolved eyes and became very good at catching prey. And then all kinds of other animals had to evolve complicated ways of avoiding being eaten, and then everything evolved!Aside from the fact that this never even touches the origin of information, their explanation assumes that there is some evolutionary mechanism capable of generating eyes, and then that there are evolutionary mechanisms capable of generating all animal body plans once eyes evolved. But there's another major problem: Simon Conway Morris thinks that the eyes of the animals in the Cambrian period couldn't see things well enough to find them easily, and so eyes couldn't have been the driver of Cambrian complexity.

There's one final explanation the video tries out -- that the Cambrian explosion was a long, slow process and the early animals were just too small to be recorded in the fossil record: "Perhaps the bilateral ancestors of today's animals were simply hiding in the shadows of the Ediacaran world until opportunity knocked."

As Stephen Meyer points out in Darwin's Doubt, there are small fossils preserved from the Ediacaran period and earlier. So size fails to explain why we don't see these Precambrian animal ancestors. In any case, the video then says: "Whatever did happen, they took that opportunity, with momentous consequences for the future."

"Whatever did happen" is right. If you want to understand the origin of information, you're going to need something capable of generating that information. Returning to the admission at the beginning of the video, from an evolutionary viewpoint that mechanism really is a "mystery." Allowing for the possibility of intelligent design, however, the answer is evident.

The design inference defined and refined

Are Hexagons Natural?

Evolution News & Views October 27, 2015 3:38 AM 

Hexagons (at least macroscopic ones) are relatively rare in nature. The most common place we see them is in beehives. It could be argued that if bees are intelligently designed, for which there is ample independent evidence, then the structures they create are also intelligently designed. We might argue that hexagons are the most efficient packing spaces for the least amount of material. We might point out that the design also provides more robust protection against stress than square-shaped cells. We can see that the structural design performs a function.

Our propensity to infer design, though, has to face up to other examples of hexagons in the non-living world. Some have been difficult to explain by natural law.

Columnar Basalt

When lava cools, it often forms polygonal-shaped columns, and hexagons are the most common shape. Many physicists have tried to understand how this occurs. There have been partial solutions, but nothing fully satisfying. Now, a paper in Physical Review Lettersreproduces the hexagonal columns with a mathematical model. The basic idea is summarized in a news release at APS Physics, along with a stunning photo of a pyramid of hexagonal basalt columns at the Giant's Causeway in Ireland. It sure looks designed. How do we make a proper inference?

The surface of cooling lava contracts more quickly than the still-warm liquid underneath, creating a stress that is relievedby the formation of cracks. Martin Hofmann from the Dresden University of Technology, Germany, and colleagues considered a uniform lava layer and calculated the energy released from different crack patterns. They found that, in the initial stages of cooling, when the cracks start to appear atrandom places on the surface, the energy release is greatest if the cracks intersect at 90-degree angles. But as the lava continues to cool and shrink, and the cracks collectively start to penetrate into the bulk, more energy is released per crack if they intersect at 120-degree angles. This transition fromindividual to collective growth of the cracks drives the pattern from rectangular to hexagonal. The hexagonal pattern is then maintained as the lava cools further, eventually leading to an array of hexagonal columns, similar to those seen in nature.

One can find columnar basalt in many locations: in the Grand Canyon, in Yellowstone Canyon, in Utah's Zion National Park, in the Rocky Mountains, at Devil's Postpile in the Sierra Nevada, and of course at the Giant's Causeway, along with other places around the world. The uniformity of the columns can be impressive, but they are rarely perfect. Many times other polygons are mixed in with the hexagons.

Saturn's North Pole Hexagon

A giant hexagon made up of clouds has persisted for decades on Saturn's north pole. This formation has baffled scientists since it was first discovered by the Voyager spacecraft in 1981. It appears to be unique in the Solar System, and it's huge: 20,000 miles across and 60 miles deep. Saturn's south pole also has a giant vortex, but not this polygonal shape. Space.com describes attempts to explain the feature:

Scientists have bandied about a number of explanations for the hexagon's origin. For instance, water swirling inside a bucket can generate whirlpools possessing holes with geometric shapes. However, there is of course no giant bucket on Saturn holding this gargantuan hexagon.

Voyager and Cassini did identify many features of this strange hexagon that could help explain how it formed. For example, the points of the hexagon rotate around its center atalmost exactly the same rate Saturn rotates on its axis. Moreover, a jet stream air current, much like the ones seen on Earth, flows eastward at up to about 220 mph (360 km/h) on Saturn, on a path that appears to follow the hexagon's outline.

We know that standing waves can maintain nodes that are stationary with respect to their reference frame. Something like that appears to be at work in Saturn's polar winds. The article says that the "bizarre giant hexagon on Saturn may finally be explained." A new model by a planetary scientist from New Mexico reproduces many of the observed properties of the hexagon.

The scientists ran computer simulations of an eastward jet flowing in a curving path near Saturn's north pole. Small perturbations in the jet -- the kind one might expect from jostling with other air currents -- made it meander into a hexagonal shape. Moreover, this simulated hexagon spun around its center at speeds close to that of the real one.

The scenario that best fits Saturn's hexagon involves shallow jets at the cloud level, study team members said. Winds below the cloud level apparently help keep the shape of the hexagon sharp and control the rate at which the hexagon drifts.

This hexagon may not be permanent, since it is subject to perturbations by processes that have no particular reason to maintain it. A simpler case is seen in Jupiter's Great Red Spot that appears to be shrinkingafter three hundred years since it was first observed.

Tiny Non-Living Hexagons

Snowflakes are classic examples of orderly structures with a hexagonal shape. Other non-living hexagons include the ring structures of many organic molecules (at least the way they are diagrammed by chemists). Some minerals also display hexagonal packing. Most of us have seen soap bubbles form hexagonal interfaces when they are packed together. An occasional hexagon can be found in mud cracks on a dry creek bed.

Life-Produced Hexagons

Bees are not the only hexagon-makers in the living world. We find hexagons on tortoise shells and in the ommatidia of insects' compound eyes. Some diatom species form free-standing hexagons in addition to the more common circles, triangles, squares, and pentagons. We humans, of course, are great hexagon-makers. Understanding their ideal packing geometry, we make them in telescope mirrors, geodesic domes, and soccer ball covers. Sometimes we create them just for their artistic value.

Proper Inferences

If humans create hexagons by intelligent design, is that true for other living things that make them? And how should we distinguish the design inference in life from the natural hexagons on Saturn or in columnar basalt? These questions provide an opportunity to understand William Dembski's Design Filter.

It's not enough that something be orderly. Casey Luskin discussed columnar basalt in 2010, answering ID critics' accusations that the Design Filter would generate a false positive. We also explained last year why snowflakes do not pass the design filter, despite their elegance and beauty. It's not enough, further, that something be rare or unique, like the Saturn hexagon. The Design Filter prefers a natural-law explanation if one can be found, or if the probability of the phenomenon's occurrence by chance is sufficiently high.

But do we wait forever for a natural explanation? Planetary scientists struggled for 35 years to explain Saturn's hexagon. Shouldn't we wait to explain beehives and compound eyes without reference to intelligent design? Isn't natural selection a natural law? (Actually, it's more like magic than a law of nature, but we'll entertain the question for the sake of argument.)

Intelligent design is not a gaps argument. It's a positive argument based on uniform experience. We have experience watching melting lava or drying mud forming geometric patterns. We have no other experience with hexagons forming on gas giants like Saturn, though. What do we do?

The Information Enigma

The short answer involves information. The hexagon on Saturn performs no function. Columnar basalt doesn't say anything. Snowflakes don't carry a message. They are mere emergent phenomena that are not that improbable, given laws of nature with which we are familiar. The Design Filter works properly by rejecting a design inference for these on the basis of probability and natural law.

All the living examples of hexagons, by contrast, are produced by codes. Beeswax will not form into hexagon cells on its own, nor will silica arrange itself into the geometric shells of diatoms. A digital code made of DNA dictates the placement of ommatidia in the insect eye and patterns in the turtle shell. Each of these structures performs a function and is the outcome of processes directed by a code.

The coded information makes use of natural laws, to be sure, but it arranges the parts into hexagons for a functional purpose. In our uniform experience, we know of one cause that can generate codes or instructions that lead to functional geometries -- intelligence.

There is one sense, though, in which we could make a design inference for the nonliving hexagons like snowflakes, basalt columns, and planetary atmospheres. Certain features of the universe are so finely tuned that without them, water, atoms, stars, and planets would not exist. It takes a higher-order design to have a universe at all.

You might even say that the elegant mathematics that allows us to describe hexagons is conceptual, not material, as are the aesthetic values that allow us to appreciate them. So even if the Design Filter rejects a design inference for some of the hexagons at one level, the mere existence of atoms, natural laws, and beauty warrants a design inference in a broader context for all of them. Without minds, we wouldn't even be debating these questions.

Darwinism Vs. Arithmetic yet again.

Proteins by Accident? Replying to a Critic of The Information Enigma

Douglas Axe October 27, 2015 9:51 AM 

Stephen Meyer and I appear in a new video from Discovery Institute, The Information Enigma, that shows how the information in DNA and proteins provides strong evidence for intelligent design. At the YouTube channel for the Center for Science & Culture, the video has generated somespirited discussion, which is good.

One commenter, who goes by the name ExtantFrodo2, has risen to the defense of Darwinism by enlisting several familiar Darwinian arguments, all of which make the evolutionary invention of new functional proteins sound much easier than it really is. The heavy use of arguments along these lines makes a response worthwhile, I think.

This excerpt from one of ExtantFrodo2's comments expresses the evolutionary thinking well:

The proteins are simply shapes. Mutation makes the shapes different. Different shapes are new tools. Some are bad & cause death to the organism. Others have no affect. Very rarely one shape turns out to be useful somewhere in the cell. It's only a metaphor to call it 'information'. DNA is a mutable template (or jig) that is cast into protein. Change the template & you change the protein. The protein may be more effective, less effective, or even completely changed (frame-shift and/or critical linkage points like di-sulfide bonds). Furthermore mutations often occur on copies or duplicates of a gene, so no former functionality (protein production) need be lost at all. As the jig or mold is transformed by mutation it produces different proteins that interact with the environment (and the cell) in new & different ways.

The first misconception here has to do with protein shapes. Since proteins are long flexible chains of linked amino acids, it's somewhat surprising that they can have fixed three-dimensional shapes at all. A strand of beads, for example, has no fixed shape. Why would a strand of amino acids be different?

In fact, the vast majority of possible protein chains are like strands of beads -- lacking any fixed shape. Life, however, makes critical use of a very special subset of the possibilities. These special proteins are coaxed into forming precise shapes by the sequence of amino acids along their chains. The process triggered by this coaxing, where a floppy protein chain rapidly acquires a well-formed structure, is known asfolding.

To give you an idea of how special these folding sequences are, theJournal of Molecular Biology paper referred to in the video estimates the proportion of chains that fold to be in the range of one in 10⁵⁰ to one in 10⁷⁴, depending on the complexity of the fold.

Even for simple folds, this means fewer than one in a trillion trillion trillion trillion amino acid sequences forms any well-defined shape at all. So the idea that every protein sequence has a shape is not at all accurate.

Secondly, the related idea that mutations merely change the shapes of proteins is equally inaccurate. The highly cooperative nature of protein folding means that it tends to be all-or-nothing. A particular protein sequence either forms structure A or it doesn't, and likewise for structure B. So for a series of mutations to convert a protein from forming structure A to forming structure B, they would first have to undothe A structure (producing a chain with no well-defined structure) and then stabilize the B structure.

In other words, changing the structure of a protein isn't nearly as easy as changing the shape of a lump of clay. The clay always has a shape, and with a little imagination we can even say the shape always represents something (which is all we ask of a lump of clay).

Proteins are different. Only highly exceptional proteins even have a shape, and these shapes are therefore fragile. Mutations are tolerated to a modest extent, after which all shape is lost.

Finally, the idea that it isn't hard to stumble upon things that are good for something, while very popular in evolutionary circles, doesn't explain the origin of exquisite things. Sure, the blobs of solder and scraps of metal or plastic you find on the floor of a workshop can be used for something -- this one a straight edge (in a pinch), that one a makeshift coaster, maybe a paperweight over there. But this make-do approach clearly doesn't work for impressive things -- not for the things we humans set out to make, and still less for the far more exquisite things we see in life.

Such things never happen by accident.

Grabbing some more of that suboptimal design I see.

To convergent evolution be the glory?

Squaring the circle?

Is Evolution Random? Answering a Common Challenge
Ann Gauger October 26, 2015 12:45 PM 

Evolutionists often challenge us for referring to Darwinian evolution as "random." They point to the fact that natural selection, the force that supposedly drives the train, always selects more "fit" organisms, and so is not random. That is only part of the story, though, and to understand why evolution can indeed be called random, the rest needs to be told.

Evolution can be considered to be composed of four parts. The first part, the grist for the mill, is the process by which mutations are generated. Generally this is thought to be a random process, with some qualifications. Single base changes occur more or less randomly, but there is some skewing as to which bases are substituted for which. Other kinds of mutations, like deletions or rearrangements or recombinations (where DNA is exchanged between chromosomes), often occur in hotspots, but not always. The net effect is that mutations occur without regard for what the organism requires, but higgledy-piggledy. In that sense mutation is random

The next part, random drift, is like a roll of the dice that decides which changes are preserved and which are lost. As the name implies, this process is also random, the result of accidental events, and without regard for the benefit of the organism. Most mutations get lost in the mix, especially when newly emerging, just because their host organisms fail to reproduce, or die from causes unrelated to genetics. It can also happen that new mutations are combined with other mutations that are harmful, and so get eliminated.

The random effects of drift are large enough to overwhelm natural selection in organisms with small breeding populations, less than a million, say. New mutations are not born fast enough to escape loss due to drift. There is a fractional threshold in the population that must be crossed before a new mutation can become "fixed," that is, universally present in every individual. A new mutation generally is lost to drift before that population threshold is crossed.

The third part, natural selection, is not random. It acts to preserve beneficial change and eliminate harmful ones. It can be said to be directional. But there are several caveats. Beneficial mutations are rare, and usually only weakly beneficial, so the effects of natural selection are not usually all that strong. Most changes provide only a slight advantage.

In addition, it can happen, and often does, that a "beneficial" mutation involves breaking something, meaning a loss of information, and a loss of potential improvement. This breaking can be irreversible for all intents and purposes. The premiere example in human evolution is that of sickle cell disease. Sickle cell disease is caused by a mutation to the hemoglobin gene that makes red blood cells resistant to the malarial parasite. In one copy the broken gene is beneficial (it increases resistance to malaria), but when two copies are present (both chromosomes carry the mutation), the red blood cells are deformed and cause painful debilitation. The broken gene is actually functionally worse than its normal version, except where malaria is present.

This brings out an important point. Natural selection does not always select the same mutations. The environment determines which mutations are favored. For example, natural selection acts to favor individuals carrying one copy of the sickle cell trait where malaria is present, but acts against the sickle cell gene where malaria is absent. So in this context, selection meanders over a fluctuating landscape of varying criteria for what is beneficial and what is not. Now it is beneficial to carry the sickle cell trait, now it is not. Different populations get favored at different times. In this sense one might say selection has a random component too, because only rarely is selection strong and unidirectional, always favoring the same mutation.

We see this variation in selection with another example, the evolution of finch beaks on the Galápagos Islands. In drought, large beaks are favored, in wet years, small beaks. The weather fluctuates, and so do the beak sizes.

Subpopulations may acquire traits, but because of environmental variation the traits do not become universal. For example, lactose intolerance -- we do not all carry the version of the gene that allows us to digest lactose as adults. Unless suddenly everyone in the world has to eat cheese as a major part of their diet, lactose intolerance won't disappear from our population.

There is a special way evolution can occur -- a sudden bottleneck in the population will tend to fix the traits that predominate in that population. Suppose a nuclear holocaust wiped out everyone except Swedes. The lactose-digesting gene would almost certainly become fixed, as would blond hair, blue eyes, and other Scandinavian traits, provided they ate cheese and lived at high latitudes. Until new mutations in new environments occurred, that would remain the case.

Now you know more about the population genetics of evolution than you imagined could be true. The sum of all these factors is what is responsible for evolution, or change over time. Mutation, drift, selection, and environmental change all play a role. Three out of these four forces are random, without regard for the needs of the organism. Even selection can be random in its direction, depending on the environment.


So tell me. Is evolution random? Most of the processes at work definitely are. Certainly evolution won't make steady progress in one direction without some other factor at work. What that factor might be remains to be seen. I personally do not think a material explanation will be found, because any process to guide evolution in a purposeful way will require a purposeful designer to create it.