Redundant no more?

Paper Finds Functional Reasons For "Redundant" Codons, Fulfilling a Prediction from Intelligent Design

Casey Luskin 

A new peer-reviewed paper in the journal Frontiers in Genetics, "Redundancy of the genetic code enables translational pausing," finds that so-called "redundant" codons may actually serve important functions in the genome. Redundant (also called "degenerate") codons are those triplets of nucleotides that encode the same amino acid. For example, in the genetic code, the codons GGU, GGC, GGA, and GGG all encode the amino acid glycine. While it has been shown (see here) that such redundancy is actually optimized to minimize the impact of mutations resulting in amino acid changes, it is generally assumed that synonymous codons are functionally equivalent. They just encode the same amino acid, and that's it.

Well, think again. The theory of intelligent design predicts that living organisms will be rich in information, and thus it encourages us to seek out new sources of functionally important information in the genome. This new paper fulfills an ID prediction by finding that synonymous codons can lead to different rates of translation that can ultimately impact protein folding and function.

This means that DNA contains multiple languages or encoded commands occupying the same string of contiguous bases. On the one hand, a string of nucleotide bases encodes amino acids. On the other hand, that same string contains information about the rate at which the ribosome should translate the protein so that it can properly fold into the right shape. The paper calls this "translational pausing." The ribosome is capable of reading both sets of commands -- as they put it, "[t]he ribosome can be thought of as an autonomous functional processor of data that it sees at its input." To put it another way, the genetic code is "multidimensional," a code within a code. This multidimensional nature exceeds the complexity of computer codes generated by humans, which lack the kind of redundancy of the genetic code. As the abstract states:

The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PI_o) purposely slows or speeds up the translation decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.

They write that the ribosome's ability to undergo translational pausing "reveal[s] the ribosome, among other things, to be not only a machine, but an independent computer-mediated manufacturing system." The paper even suggests, "Cause-and-effect physical determinism...cannot account for the programming of sequence-dependent biofunction."

Apart from ID's expectation of finding new layers of information in the genome, the paper implicitly challenges some common evolutionary assumptions. The notion that shared synonymous codons are functionally irrelevant has been used to buttress arguments for Darwinian evolution.

For one thing, some evolutionists claim that phylogenetic signals can be carried by the distribution of synonymous codons since they're functionally equivalent. This paper suggests otherwise.

For another, seeking to infer the activity of natural selection, evolutionary biologists statistically analyze the frequency of synonymous (thought to be functionally unimportant) and nonsynonymous (thought to be functionally important) codons in a gene. (We've discussed this previously here andhere.) As the thinking goes, if synonymous codons are functionally unimportant, then three conclusions may follow: a bias toward synonymous codons implies purifying selection in the gene, a bias towards nonsynonymous codons implies positive selection, and an equal balance implies neutral evolution (no selection). But if synonymous codons can have important functional meaning, then the whole methodology goes out the window, and hundreds of studies that used these methods to infer "selection" during the supposed "evolution of genes" could be wrong.

The evidence supports the view that synonymous codons have divergent effects upon translation, as the paper finds: "Data shows that with fixed levels of tRNA's, synonymously encoded mRNA's translate with different speeds" and "Recent work has built on the above observations showing a strong relationship between specific arrangements of codons in mRNA to the rate of translation." Genetic modifications in the lab can even induce translational pausing:

"Pausingfunction" is caused by specific mRNA codon sequences rather than by tunnel-protein interactions to amino acid sequences. This contention is supported by data involving the substitution of rare codons with synonymous codons in E. coli. If the pausing effect was solely related to the amino acid chain sequence, then replacing codons with synonymous codons should still produce the same folded amino acid chain with the same translation speed. However, substitution of rare codons with synonymous codons did produce a change in speed and conformation changes.

These changes in translational speed can have phenotypic effects:

For example, a silent mutation in the human gene ABCB1 caused a conformational change to occur in the P-glycoprotein. This protein folded differently caused by a temporal change in translation affecting the timing of the folding process. ... Thus, the protein folding pathways are affected by changes in the coding regions of DNA" (internal citations removed).

In short, "redundant" codons are not necessarily redundant at all. As the paper puts it: "we show why the term "degeneracy" is completely inappropriate. The dual coding functionality of redundancy is anything but 'degenerate.' It represents, instead, far more sophistication, layers, and dimensions of formal prescription." In fact, this paper "defines new universal linguistic-like rules needed to identify and characterize codon mappings of TP events." The authors write:

The TP code exhibits distinct meaning in relation to mappings between codons and pausing units. The TP code also exhibits a syntax or grammar that obeys strict codon relationships that demonstrate language properties. Because of the redundancy of the genetic code, it could be argued that the TP language is a subset of the genetic language. The subspace of the TP language resides, and thus appears to have a dependency on, the primary genetic code. Within this subspace, however, we argue that the TP language is decoupled from and remains independent of the protein-coding language.

Their conclusion about the high-information capacity of the genetic code is striking:

Redundancy in the primary genetic code allows for additional independent codes. Coupled with the appropriate interpreters and algorithmic processors, multiple dimensions of meaning, and function can be instantiated into the same codon string. We have shown a secondary code superimposed upon the primary codonic prescription of amino acid sequence in proteins. Dual interpretations enable the assembly of the protein's primary structure while enabling additional folding controls via pausing of the translation process. TP provides for temporal control of the translation process allowing the nascent protein to fold appropriately as per its defined function. This duality in the coding function acts to reduce the redundancy in the genetic code when viewed holistically. The functionality of condonic redundancy denies the ill-advised label of "degeneracy." When simultaneously combined with other coding schemas such as intron/exon boundary conditions, and overlapping and oppositely oriented promoters, multiple dimensions of independent coding by the same codon string has become apparent.

In his 2001 book No Free Lunch, William Dembski explained the primary prediction of intelligent design:

[W]hat about the predictive power of intelligent design? Intelligent design offers one obvious prediction, namely, that nature should be chock-full of specified complexity and therefore should contain numerous pointers to design ... This prediction is increasingly being confirmed. (p. 362)

Multidimensional codes and new levels of specified complexity are exactly what ID predicts, and they're exactly what this paper is reporting. It's this sort of sophisticated, information-rich control that is expected by intelligent design, in contrast to Darwinian biology which fails to anticipate it. On the contrary, Darwinian advocates publish mountains of papers banking upon the unquestioned assumption that there is no important, functional reason for the existence of "redundant" or "degenerate" features. Slowly but surely, the data are turning the tide in the evolution debate.

A mathematical examination of attempts to reduce consciousness to physics.

From Barren Planet to Civilization — Four Simple Steps

Granville Sewell

In the video “Why Evolution is Different,” above, I make the simple point that to not believe in intelligent design, you have to believe that the four fundamental, unintelligent forces of physics alone (the gravitational, electromagnetic, and strong and weak nuclear forces) could have rearranged the fundamental particles of physics into encyclopedias and science texts and computers and airplanes and Apple iPhones. I show that this belief runs contrary to the more general statements of the second law of thermodynamics, even if the Earth is an open system.

Whether or not it has anything to do with the second law, I can’t imagine anything in all of science that is more clear and more obvious than that unintelligent forces alone cannot produce such things as Apple iPhones. Yet materialists are not impressed. They believe they can explain how unintelligent forces alone could produce computers and airplanes. In the video, I outline the four steps in the materialists’ explanation of how advanced civilizations can spontaneously arise on barren planets, without design:

Three or four billion years ago a collection of atoms formed by pure chance that was able to duplicate itself.

These complex collections of atoms were able to preserve their complex structures and pass them on to their descendants, generation after generation.

Over a long period of time, the accumulation of duplication errors resulted in more and more elaborate collections of atoms.

Eventually something called “intelligence” allowed some of these collections of atoms to design buildings and computers and airplanes, and write encyclopedias and science texts.

The first step is the origin of life: even most materialists will admit that this is a very difficult problem which has not yet been solved by science. Regarding the fourth step, we may feel that we “understand” how humans design and build computers and airplanes, because we see it happen and perhaps even do such things ourselves. But seeing something happen and understanding how it happens are two very different things, and again I think even most materialists will agree that science cannot yet explain human consciousness or intelligence in terms of unintelligent forces alone.

Darwinists claim that the third step is well understood by science, that natural selection has organized these duplication errors into higher animals, and intelligent humans. The second part of my video disputes this claim, and argues that what we see in the fossil record — large gaps where major new features appear — actually looks more like the way human technology, such as software or automobiles, “evolves,” through testing and improvements.

When I point out, as I do in the second part of the video, the striking similarities between the evolution of life and the evolution of human technology such as the automobile, some people have responded by saying that of course cars cannot evolve like animals, because they cannot reproduce, so there are no “variations” for natural selection to work with. Actually the fact that natural selection cannot act on cars is irrelevant to the main point of this comparison, which is simply that similarities between “species” (of cars or animals) do not prove the absence of design.

However, even though it is irrelevant to my main point, let’s look at the argument that evolution is easier to explain if there is reproduction, because that brings us to the second step of the materialists’ explanation. That the third step seems even superficially plausible (until we look at it in more detail) depends completely on the second step, the fact that living things are able to reproduce, that “these complex collections of atoms are able to preserve their complex structures and pass them on to their descendants, generation after generation.”

Reproduction is the most fundamental characteristic of life. We see it happen everywhere, so we may feel there is no mystery to reproduction. But again, seeing something happen and explaining how it happens naturally are two very different things. Is it really true that if cars were able to give birth to other cars — that is, if they were able to reproduce themselves almost perfectly (the copies even retaining the ability to reproduce themselves in turn), with occasional minor errors — that would make the evolution of cars easier to explain without design than if individual cars experienced slight changes or improvements directly, through rust or crashes or other natural causes?

We are so used to seeing animals make nearly perfect copies of themselves that we dismiss this as just another “natural” process. However, if we actually saw cars that contained car-building factories inside with the ability to construct new cars — not just normal new cars, but new cars containing car-building factories — maybe we would realize what an astonishing process reproduction really is, and we might conclude that this would actually make automobile evolution even more amazing and even more difficult to explain without design.

Mathematicians are trained to value simplicity. When we have a clear, simple, proof of a theorem, and a long, complicated counterargument, involving controversial and unproven assertions, we accept the clear, simple, proof, and we know there must be errors in the counterargument even before we find them. The argument here for intelligent design could not be simpler or clearer: unintelligent forces of physics alone cannot rearrange atoms into computers and airplanes and Apple iPhones. And the counterargument consists of four steps, each of which — to put it very generously — is full of dubious and unproven assertions.

On removing ego from the equation(or not).

"Science Signaling"
David Klinghoffer March 24, 2016 11:42 AM

I keep circling back in my mind to the dramatic juxtaposition of atheist, theistic evolutionist (TE), and ID advocate in Saturday night's debate at the University of Toronto. I won't use names, since it was almost a clash of archetypes where the personal identities and personal circumstances hardly matter. That the TE persistently joined with the atheist in going after the ID'er speaks volumes.

An email correspondent, thinking along the same lines, offers the phrase "science signaling," a play on "virtue signaling." The latter refers to the habit of some in political and other debates to care more about signaling their own virtue than about winning the election or other contest against an opponent. The currency is feeling special and impressing strangers, not actually accomplishing anything.

In science signaling, the point is to signal that you're on the prestige side of any controversy. The theistic evolutionist in Saturday's event was true to type for many TE advocates. He seemed eager, pathetically so, to show the atheist that he "resonated" with him. While unctuously assuring the ID'er that they were on the same side spiritually (as "brothers in Christ"), even as the ID advocate talked science only and not religion, the TE's focus appeared to be on sharing some of the reflected prestige of the atheist scientist. He also did a fair amount of piety signaling to demonstrate to religious believers in the audience that, despite the seeming overlap with the atheist position, he's a strong Christian.

In this respect, for the theistic evolutionist, the science is almost beside the point. It's more of a tool for securing status, which may explain why TEs, like atheists, rarely grapple with the science of intelligent design. Science for many of them is a mask for pursuing other things.

Coincidentally, as I write this it's the Jewish holiday of Purim, when we read the Book of Esther. A custom is the wearing of masks and other costumes. Esther is a surprisingly secular and political story. That being the case, you naturally look for contemporary relevance. This year I'm struck, in the relationship between obsequious courtier Haman and the more ambivalent figure of foolish King Ahasuerus, by the pervasive theme of pride, prestige, status, craving for recognition, delight in royal recognition, and prestige by transference. Take 20 minutes and read it for yourself. You don't need to be religious to appreciate the astute psychology.

Much of the plot is about the ability of prominent, powerful people to take violent offense at having their status slighted. So violent that there must be a scapegoat -- whether the deposed Queen Vashti, or the unprotected Jews, whose scattered communities Haman wishes to see destroyed, all to assuage a bruised ego.

Try to name a contentious matter in science, politics, entertainment, and more that isn't fueled, at least on one side -- just behind the mask -- by status and threats to status. For example, how often does "defending science" really mean "defending or advancing your own sense of personal prestige"? Quite often.

In mainstream media coverage of the evolution debate, where a superficial grasp of the issues involved is almost an ironclad rule, 95 percent of what's said against intelligent design is about signaling, not science. It's a mask for other things.

On paradise:The Watchtower Society's commentary.

PARADISE

A beautiful park, or a parklike garden. The Greek word pa·ra′dei·sos occurs three times in the Christian Greek Scriptures. (Lu 23:43; 2Co 12:4; Re 2:7) Greek writers as far back as Xenophon (c. 431-352 B.C.E.) used the word (pairidaeza), and Pollux attributed it to Persian sources. (Cyropaedia, I, iii, 14; Anabasis, I, ii, 7; Onomasticon, IX, 13) Some lexicographers would derive the Hebrew word par·des′ (meaning, basically, a park) from the same source. But since Solomon (of the 11th century B.C.E.) used par·des′ in his writings, whereas existing Persian writings go back only to about the sixth century B.C.E., such derivation of the Hebrew term is only conjectural. (Ec 2:5; Ca 4:13) The remaining use of par·des′ is at Nehemiah 2:8, where reference is made to a royal wooded park of Persian King Artaxerxes Longimanus, in the fifth century B.C.E.—See PARK.

The three terms (Hebrew par·des′, Persian pairidaeza, and Greek pa·ra′dei·sos), however, all convey the basic idea of a beautiful park or parklike garden. The first such park was that made by man’s Creator, Jehovah God, in Eden. (Ge 2:8, 9, 15) It is called a gan, or “garden,” in Hebrew but was obviously parklike in size and nature. The Greek Septuagint appropriately uses the term pa·ra′dei·sos with reference to that garden. (See EDEN No. 1; GARDEN [Garden of Eden].) Because of sin, Adam lost his right to live in that paradise and his opportunity to gain the right to everlasting life, which right was represented in the fruit of a divinely designated tree in the center of the garden. The garden of Eden may have been enclosed in some way, since it was necessary to place angelic guards only at the east side thereof to prevent human entrance.—Ge 3:22-24.

What is the Paradise that Jesus promised to the evildoer who died alongside him?

Luke’s account shows that an evildoer, being executed alongside Jesus Christ, spoke words in Jesus’ defense and requested that Jesus remember him when he ‘got into his kingdom.’ Jesus’ reply was: “Truly I tell you today, You will be with me in Paradise.” (Lu 23:39-43) The punctuation shown in the rendering of these words must, of course, depend on the translator’s understanding of the sense of Jesus’ words, since no punctuation was used in the original Greek text. Punctuation in the modern style did not become common until about the ninth century C.E. Whereas many translations place a comma before the word “today” and thereby give the impression that the evildoer entered Paradise that same day, there is nothing in the rest of the Scriptures to support this. Jesus himself was dead and in the tomb until the third day and was then resurrected as “the firstfruits” of the resurrection. (Ac 10:40; 1Co 15:20; Col 1:18) He ascended to heaven 40 days later.—Joh 20:17; Ac 1:1-3, 9.

The evidence is, therefore, that Jesus’ use of the word “today” was not to give the time of the evildoer’s being in Paradise but, rather, to call attention to the time in which the promise was being made and during which the evildoer had shown a measure of faith in Jesus. It was a day when Jesus had been rejected and condemned by the highest-ranking religious leaders of his own people and was thereafter sentenced to die by Roman authority. He had become an object of scorn and ridicule. So the wrongdoer alongside him had shown a notable quality and commendable heart attitude in not going along with the crowd but, rather, speaking out in Jesus’ behalf and expressing belief in his coming Kingship. Recognizing that the emphasis is correctly placed on the time of the promise’s being made rather than on the time of its fulfillment, other translations, such as those in English by Rotherham and Lamsa, those in German by Reinhardt and W. Michaelis, as well as the Curetonian Syriac of the fifth century C.E., rendered the text in a form similar to the reading of the New World Translation, quoted herein.

As to the identification of the Paradise of which Jesus spoke, it is clearly not synonymous with the heavenly Kingdom of Christ. Earlier that day entry into that heavenly Kingdom had been held out as a prospect for Jesus’ faithful disciples but on the basis of their having ‘stuck with him in his trials,’ something the evildoer had never done, his dying on a stake alongside Jesus being purely for his own criminal acts. (Lu 22:28-30; 23:40, 41) The evildoer obviously had not been “born again,” of water and spirit, which Jesus showed was a prerequisite to entry into the Kingdom of the heavens. (Joh 3:3-6) Nor was the evildoer one of the ‘conquerors’ that the glorified Christ Jesus stated would be with him on his heavenly throne and that have a share in “the first resurrection.”—Re 3:11, 12, 21; 12:10, 11; 14:1-4; 20:4-6.

Some reference works present the view that Jesus was referring to a paradise location in Hades or Sheol, supposedly a compartment or division thereof for those approved by God. The claim is made that the Jewish rabbis of that time taught the existence of such a paradise for those who had died and were awaiting a resurrection. Regarding the teachings of the rabbis, Hastings’ Dictionary of the Bible states: “The Rabbinical theology as it has come down to us exhibits an extraordinary medley of ideas on these questions, and in the case of many of them it is difficult to determine the dates to which they should be assigned. . . . Taking the literature as it is, it might appear that Paradise was regarded by some as on earth itself, by others as forming part of Sheol, by others still as neither on earth nor under earth, but in heaven . . . But there is some doubt as respects, at least, part of this. These various conceptions are found indeed in later Judaism. They appear most precisely and most in detail in the mediaeval Cabbalistic Judaism . . . But it is uncertain how far back these things can be carried. The older Jewish theology at least . . . seems to give little or no place to the idea of an intermediate Paradise. It speaks of a Gehinnom for the wicked, and a Gan Eden, or garden of Eden, for the just. It is questionable whether it goes beyond these conceptions and affirms a Paradise in Sheol.”—1905, Vol. III, pp. 669, 670.

Even if they did teach such a thing, it would be most unreasonable to believe that Jesus would propagate such a concept, in view of his condemnation of the non-Biblical religious traditions of the Jewish religious leaders. (Mt 15:3-9) Likely the paradise truly familiar to the Jewish malefactor to whom Jesus spoke was the earthly Paradise described in the first book of the Hebrew Scriptures, the Paradise of Eden. That being so, Jesus’ promise would reasonably point to a restoration of such earthly paradisaic condition. His promise to the wrongdoer would therefore give assured hope of a resurrection of such an unrighteous one to an opportunity to life in that restored Paradise.—Compare Ac 24:15; Re 20:12, 13; 21:1-5; Mt 6:10.

A Spiritual Paradise. Throughout many of the prophetic books of the Bible, divine promises are found regarding the restoration of Israel from the lands of its exile to its desolated homeland. God would cause that abandoned land to be tilled and sown, to produce richly, and to abound with humankind and animalkind; the cities would be rebuilt and inhabited, and people would say: “That land yonder which was laid desolate has become like the garden of Eden.” (Eze 36:6-11, 29, 30, 33-35; compare Isa 51:3; Jer 31:10-12; Eze 34:25-27.) However, these prophecies also show that paradise conditions related to the people themselves, who, by faithfulness to God, could now “sprout” and flourish as “trees of righteousness,” enjoying beautiful spiritual prosperity like a “well-watered garden,” showered by bounteous blessings from God because of having his favor. (Isa 58:11; 61:3, 11; Jer 31:12; 32:41; compare Ps 1:3; 72:3, 6-8, 16; 85:10-13; Isa 44:3, 4.) The people of Israel had been God’s vineyard, his planting, but their badness and apostasy from true worship had caused a figurative ‘withering away’ of their spiritual field, even before the literal desolation of their land took place.—Compare Ex 15:17; Isa 5:1-8; Jer 2:21.

This undoubtedly provides the key for understanding Paul’s description of the vision (evidently had by him, since it forms part of his defense of his own apostleship) referred to at 2 Corinthians 12:1-7. Caught away to “the third heaven” (see HEAVEN [Third Heaven]), the vision viewer entered “paradise” and heard unutterable words. That this paradise envisioned could refer to a spiritual state among God’s people, as in the case of fleshly Israel, can be seen from the fact that the Christian congregation was also God’s “field under cultivation,” his spiritual vineyard, rooted in Christ Jesus and bearing fruit to God’s praise. (1Co 3:9; Joh 15:1-8) As such it had replaced the nation of Israel in God’s favor. (Compare Mt 21:33-43.) Paul’s vision, nevertheless, must logically have applied to some future time, so as to constitute a ‘revelation.’ (2Co 12:1) An apostasy was due to set in among the Christian congregation and was already working in Paul’s day; it would result in a condition like that of a field oversown with weeds. (Mt 13:24-30, 36-43; Ac 20:29; 2Th 2:3, 7; compare Heb 6:7, 8.) So, Paul’s paradise vision would not reasonably apply while such was the case but would evidently relate to the time of “the harvest season” when the genuine Christians would be gathered by the angelic reapers and would enjoy rich blessings and spiritual prosperity from God.

It is evident, however, that the restoration prophecies recorded by the Hebrew prophets include elements that will also find a physical fulfillment in the restored earthly Paradise. There are features, for example, in Isaiah 35:1-7, such as the healing of the blind and the lame, that did not have a literal fulfillment following the restoration from ancient Babylon, nor are they fulfilled in such a manner in the Christian spiritual paradise. It would be inconsistent for God to inspire such prophecies as those of Isaiah 11:6-9, Ezekiel 34:25, and Hosea 2:18, with the intention that they have only a figurative or spiritual meaning, without having a literal fulfillment of these things in the physical experiences of God’s servants.

Eating in “the Paradise of God.” Revelation 2:7 mentions a “tree of life” in “the paradise of God” and that eating from it would be the privilege of the one “that conquers.” Since other promises given in this section of Revelation to such conquering ones clearly relate to their gaining a heavenly inheritance (Re 2:26-28; 3:12, 21), it seems evident that “the paradise of God” in this case is a heavenly one. The word “tree” here translates the Greek word xy′lon, which literally means “wood,” and could therefore refer to an orchard of trees. In the earthly Paradise of Eden, eating of the tree of life would have meant living forever for man. (Ge 3:22-24) Even the fruit of the other trees of the garden would have been life sustaining for man as long as he continued obedient. So, the partaking of “the tree [or trees] of life” in “the paradise of God” evidently relates to the divine provision for sustained life granted the Christian conquerors, other texts showing that they receive the prize of immortality and incorruptibility along with their heavenly Head and Lord, Christ Jesus.—1Co 15:50-54; 1Pe 1:3, 4.

That simple beginning now dead and buried?

Subcellular Map of the Human Proteome Reveals “Highly Complex Architecture”
Cornelius Hunter

New research is using antibodies to map out the spatio-temporal locations of 12,003 different proteins in human cells. The results are another example of how, as Bruce Alberts  put it in 1998, “We have always underestimated cells.”

Alberts explained how cells were once naïvely viewed as something of a haphazard affair, where molecules “were thought to diffuse freely, randomly colliding.” The new research reveals the “the highly complex architecture of the human cell” and adds more detail to the fact that the workings of the cell are far from random:

A total of 12,003 proteins targeted by 13,993 antibodies were classified into one or several of 30 cellular compartments and substructures, altogether defining the proteomes of 13 major organelles.

Although evolutionists  “thought the cell was so simple,” this research is showing that the “cellular proteome is compartmentalized and spatiotemporally regulated to a high degree.” In fact “[m]ore than half of these 12,003 proteins localize in more than one compartment at the same time.” This is consistent with the fact that most proteins are capable of performing multiple functions , and is another indicator of high complexity:

Moreover, proteins that localize to more than one compartment may have context-specific functions, increasing the functionality of the proteome. The fact that proteins “moonlight” in different parts of the cell is now well accepted. … The more complex a system is, the greater the number of parts that must be sustained in their proper place, and the lesser the tolerance for errors; therefore, a high degree of regulation and control is required.

Indeed, the degree of regulation and control required for this system is not only enormous, but contrary to evolutionary expectations.

On Darwinism v. the real world.

Glicksman: Raising the Bar for Darwinism
David Klinghoffer | @d_klinghoffer

“How can you understand where life came from if you don’t understand how it actually works?” So asks Dr. Howard Glicksman, physician and author of the 81-part Evolution News series “The Designed Body,” in a new ID the Future episode. Download the podcast here, or listen to it here.

Glicksman chats with Discovery Institute biologist Ray Bohlin about the origins of his series in his own clinical practice, and why he decided to “raise the bar for Darwinism” by confronting evolutionists with the irreducible complexity of how the body, with its many systems and subsystems, works in detail. It’s a subject that tends to get brushed aside in evolutionary theorizing. Dr. Glicksman and Dr. Bohlin then turn to a fascinating discussion of a case in point: the human calcium control system.

On the sacred name in the new testament:The Watchtower Society's commentary.

Should the Name Jehovah Appear in the New Testament?

DOES it matter whether God’s name appears in the Bible? God obviously felt so. His name, as represented by the four Hebrew characters known as the Tetragrammaton, appears almost 7,000 times in the original Hebrew text of what is commonly called the Old Testament. *

Bible scholars acknowledge that God’s personal name appears in the Old Testament, or Hebrew Scriptures. However, many feel that it did not appear in the original Greek manuscripts of the so-called New Testament.

What happens, then, when a writer of the New Testament quotes passages from the Old Testament in which the Tetragrammaton appears? In these instances, most translators use the word “Lord” rather than God’s personal name. The New World Translation of the Holy Scriptures does not follow this common practice. It uses the name Jehovah 237 times in the Christian Greek Scriptures, or New Testament.

What problems do Bible translators face when it comes to deciding whether to use God’s name in the New Testament? What basis is there for using God’s name in this part of the Holy Scriptures? And how does the use of God’s name in the Bible affect you?

A Translation Problem:

The manuscripts of the New Testament that we possess today are not the originals. The original manuscripts written by Matthew, John, Paul, and others were well used, and no doubt they quickly wore out. Hence, copies were made, and when those wore out, further copies were made. Of the thousands of copies of the New Testament in existence today, most were made at least two centuries after the originals were penned. It appears that by that time those copying the manuscripts either replaced the Tetragrammaton with Kuʹri·os or Kyʹri·os, the Greek word for “Lord,” or copied from manuscripts where this had been done. *

Knowing this, a translator must determine whether there is reasonable evidence that the Tetragrammaton did in fact appear in the original Greek manuscripts. Is there any such proof? Consider the following arguments:

When Jesus quoted the Old Testament or read from it, he used the divine name. (Deuteronomy 6:13, 16; 8:3; Psalm 110:1; Isaiah 61:1, 2; Matthew 4:4, 7, 10; 22:44; Luke 4:16-21) In the days of Jesus and his disciples, the Tetragrammaton appeared in copies of the Hebrew text of what is often called the Old Testament, as it still does today. However, for centuries scholars thought that the Tetragrammaton was absent from manuscripts of the Greek Septuagint translation of the Old Testament, as well as from manuscripts of the New Testament. Then in the mid-20th century, something remarkable came to the attention of scholars—some very old fragments of the Greek Septuagint version that existed in Jesus’ day had been discovered. Those fragments contain the personal name of God, written in Hebrew characters.

Jesus used God’s name and made it known to others. (John 17:6, 11, 12, 26) Jesus  plainly stated: “I have come in the name of my Father.” He also stressed that his works were done “in the name of [his] Father.” In fact, Jesus’ own name means “Jehovah Is Salvation.”—John 5:43; 10:25.

The divine name appears in its abbreviated form in the Greek Scriptures. At Revelation 19:1, 3, 4, 6, the divine name is embedded in the expression “Alleluia,” or “Hallelujah.” This expression literally means “Praise Jah, you people!” Jah is a contraction of the name Jehovah.

Early Jewish writings indicate that Jewish Christians used the divine name in their writings. The Tosefta, a written collection of oral laws completed by about 300 C.E., says with regard to Christian writings that were burned on the Sabbath: “The books of the Evangelists and the books of the minim [thought to be Jewish Christians] they do not save from a fire. But they are allowed to burn where they are, . . . they and the references to the Divine Name which are in them.” This same source quotes Rabbi Yosé the Galilean, who lived at the beginning of the second century C.E., as saying that on other days of the week “one cuts out the references to the Divine Name which are in them [the Christian writings] and stores them away, and the rest burns.” Thus, there is strong evidence that the Jews living in the second century C.E. believed that Christians used Jehovah’s name in their writings.

How Have Translators Handled This Issue?

Is the New World Translation the only Bible that restores God’s name when translating the Greek Scriptures? No. Based upon the above evidence, many Bible translators have felt that the divine name should be restored when they translate the New Testament.

For example, many African, American, Asian, and Pacific-island language versions of the New Testament use the divine name liberally. (See chart on page 21.) Some of these translations have appeared recently, such as the Rotuman Bible (1999), which uses the name Jihova 51 times in 48 verses of the New Testament, and the Batak-Toba version (1989) from Indonesia, which uses the name Jahowa 110 times in the New Testament. The divine name has appeared, too, in French, German, and Spanish translations. For instance,  Pablo Besson translated the New Testament into Spanish in the early 20th century. His translation uses Jehová at Jude 14, and nearly 100 footnotes suggest the divine name as a likely rendering.

Below are some examples of English translations that have used God’s name in the New Testament:

A Literal Translation of the New Testament . . . From the Text of the Vatican Manuscript, by Herman Heinfetter (1863)

The Emphatic Diaglott, by Benjamin Wilson (1864)

The Epistles of Paul in Modern English, by George Barker Stevens (1898)

St. Paul’s Epistle to the Romans, by W. G. Rutherford (1900)

The Christian’s Bible—New Testament, by George N. LeFevre (1928)

The New Testament Letters, by J.W.C. Wand, Bishop of London (1946)

Recently, the 2004 edition of the popular New Living Translation made this comment in its preface under the heading “The Rendering of Divine Names”: “We have generally rendered the tetragrammaton (YHWH) consistently as ‘the LORD,’ utilizing a form with small capitals that is common among English translations. This will distinguish it from the name ʹadonai, which we render ‘Lord.’” Then when commenting on the New Testament, it says: “The Greek word kurios is consistently translated ‘Lord,’ except that it is translated ‘LORD’ wherever the New  Testament text explicitly quotes from the Old Testament, and the text there has it in small capitals.” (Italics ours.) The translators of this Bible therefore acknowledge that the Tetragrammaton (YHWH) should be represented in these New Testament quotes.

Interestingly, under the heading “Tetragrammaton in the New Testament,” The Anchor Bible Dictionary makes this comment: “There is some evidence that the Tetragrammaton, the Divine Name, Yahweh, appeared in some or all of the O[ld] T[estament] quotations in the N[ew] T[estament] when the NT documents were first penned.” And scholar George Howard says: “Since the Tetragram was still written in the copies of the Greek Bible [the Septuagint] which made up the Scriptures of the early church, it is reasonable to believe that the N[ew] T[estament] writers, when quoting from Scripture, preserved the Tetragram within the biblical text.”

Two Compelling Reasons:

Clearly, then, the New World Translation was not the first Bible to contain the divine name in the New Testament. Like a judge who is called upon to decide a court case for which there are no living eyewitnesses, the New World Bible Translation Committee carefully weighed all the relevant evidence. Based on the facts, they decided to include Jehovah’s name in their translation of the Christian Greek Scriptures. Note two compelling reasons why they did so.

(1) The translators believed that since the Christian Greek Scriptures were an inspired addition to the sacred Hebrew Scriptures, the sudden disappearance of Jehovah’s name from the text seemed inconsistent.

Why is that a reasonable conclusion? About the middle of the first century C.E., the disciple James said to the elders in Jerusalem: “Symeon has related thoroughly how God for the first time turned his attention to the nations to take out of them a people for his name.” (Acts 15:14) Does it sound logical to you that James would make such a statement if nobody in the first century knew or used God’s name?

(2) When copies of the Septuagint were discovered that used the divine name rather than Kyʹri·os (Lord), it became evident to the translators that in Jesus’ day copies of the earlier Scriptures in Greek—and of course those in Hebrew—did contain the divine name.

Apparently, the God-dishonoring tradition of removing the divine name from Greek manuscripts developed only later. What do you think? Would Jesus and his apostles have promoted such a tradition?—Matthew 15:6-9.

Call “on the Name of Jehovah”

Really, the Scriptures themselves act as a conclusive “eyewitness” statement that early Christians did in fact use Jehovah’s name in their writings, especially when they quoted passages from the Old Testament that contain that name. Without a doubt, then, the New World Translation has a clear basis for restoring the divine name, Jehovah, in the Christian Greek Scriptures.

How does this information affect you? Quoting the Hebrew Scriptures, the apostle Paul reminded the Christians in Rome: “Everyone who calls on the name of Jehovah will be saved.” Then he asked: “How will they call on him in whom they have not put faith? How, in turn, will they put faith in him of whom they have not heard?” (Romans 10:13, 14; Joel 2:32) Bible translations that use God’s name when appropriate help you to draw close to God. (James 4:8) Really, what an honor it is for us to be allowed to know and to call upon God’s personal name, Jehovah.

A TRANSLATOR WHO RESPECTED GOD’S NAME

In November 1857, Hiram Bingham II, a 26-year-old missionary, arrived with his wife in the Gilbert Islands (now called Kiribati). The missionary ship on which they had traveled was sponsored by meager donations from American Sunday School children. It had been named the Morning Star by its sponsors to reflect their belief in the coming Millennium.

“Physically, Bingham was not strong,” states Barrie Macdonald in his book Cinderellas of the Empire. “He suffered from frequent bowel ailments, and from chronic throat trouble which affected his ability to speak in public; his eyesight was so weak that he could only spend two or three hours a day reading.”

However, Bingham set his mind to learning the Gilbertese language. This was not an easy task. He started by pointing at objects and asking their names. When he had collected a list of some two thousand words, he paid one of his converts a dollar for every one hundred new words he could add to the list.

Bingham’s perseverance paid off. By the time he had to leave the Gilbert Islands in 1865 because of his deteriorating health, he not only had given the Gilbertese language a written form but had also translated the books of Matthew and John into Gilbertese. When he returned to the islands in 1873, he brought with him the completed translation of the New Testament in Gilbertese. He persevered for a further 17 years and by 1890 completed the translation of the entire Gilbertese Bible.

Bingham’s translation of the Bible is in use in Kiribati to this day. Those reading it will notice that he used Jehovah’s name (Iehova in Gilbertese) thousands of times in the Old Testament as well as over 50 times in the New Testament. Truly, Hiram Bingham was a translator who respected God’s name!

Finally,permission to examine the books?

State Action on Science Education: 2017 in a Nutshell
Sarah Chaffee

With the legislative season finished, I would like to take a moment to review progress this year toward better evolution education in K-12 public schools.

This year saw a growing movement by policymakers across the country to defend academic freedom to present the evidence for and against evolution. Two state legislative bodies commended academic freedom for teachers, Texas overcame attempts to gut their science standards on evolution, and other states took action regarding academic freedom as well.

In resolutions this legislative season, Alabama and Indiana both went on record in favor of academic freedom.

In May, Alabama’s Senate adopted House Joint Resolution 78. While not legally binding, it officially encourages authorities not to prohibit public school teachers from “helping students understand, analyze, critique, and review” the strengths and weaknesses of scientific theories, so long as teaching falls within the State Board of Education’s curriculum framework.

Similarly, the Indiana Senate passed Senate Resolution 17,  encouraging discussion of the spectrum of scientific viewpoints on evolution. Referencing language from the 2001 No Child Left Behind Act Conference Report, it also urged the Indiana Department of Education “to reinforce support of teachers who choose to teach a diverse curriculum.”

Both resolutions are good news for teachers who want to pursue academic excellence in science teaching.

Meanwhile the Texas Board of Education rebuffed the Darwin-only crowd’s attempt to water down their state science standards on evolution. The board adopted streamlined biology standards, Texas Essential Knowledge and Skills (TEKS), in April, requiring students to apply analytical reasoning to the evidence about Darwinian evolution.

“The streamlined TEKS in biology continue to call for critical thinking in the study of theories such as evolution,” Board of Education member Barbara Cargill said. “It is obvious that the intent is for students to apply these critical thinking skills to the various scientific theories about the origin of life.”

Other states made progress as well. In Oklahoma, South Dakota, and Texas, academic freedom bills were introduced or made it through various stages of the legislative process, though none were passed. Louisiana adopted revised science astandards and placed the entirety of the Louisiana Science Education Act (a 2008 academic freedom law) into the introduction of the standards.

Remember that old saying about stuff that goes around?

Dawkins (Not) at Berkeley – The Best Irony
David Klinghoffer | @d_klinghoffer

On the story about evolutionary atheist Richard Dawkins getting disinvited as an event speaker by a progressive Berkeley radio station (see  here and here), Discovery Institute chairman of the board Bruce Chapman points out the best irony. While Dawkins protests his “de-platforming” over past comments on Islam, in 2009 he helped get Ben Stein de-platformed as a commencement speaker at the University of Vermont over — you guessed it — Stein’s take on evolution and his role in the film  Expelled.

The New York Times talked with Dawkins and got this complaint from him.

“Many people are saying this is a freedom of speech issue, and of course it is,” he said. “But it’s actually more of a freedom of listening issue. People bought tickets because they wanted to hear me.”

They give the larger context:

In recent months, the cancellation of speeches on college campuses has stirred debates over balancing free speech and security concerns.

Berkeley has been a particular focus.

The Center for Inquiry, which includes the Richard Dawkins Foundation for Reason & Science, echoed Dawkins, saying it was “stunned and deeply dismayed.”

The public radio station, KPFA, explained that it withdrew the invitation to speak after realizing Dawkins had expressed controversial views about the Muslim religion. In the incident with Stein, the University of Vermont’s then-president Daniel Fogel explained that they got cold feet after realizing Stein had expressed controversial views about the theory of evolution.

From President Fogel’s statement in a  UVM press release:

As you may know, Mr. Stein delivered an excellent Kalkin lecture on our campus last year, focused primarily on economic issues, to which our students responded warmly and enthusiastically. It was on the basis of that experience that I extended him an invitation to be our Commencement speaker.

Mr. Stein has also expressed opinions on subjects unrelated to economics, most notably with respect to evolutionary theory, intelligent design, and the role of science in the Holocaust. Those views are highly controversial, to say the least. Following the announcement of Mr. Stein as Commencement speaker, profound concerns have been expressed to me by persons both internal and external to the University about his selection. Once I apprised Mr. Stein of these communications, he immediately and most graciously declined our Commencement invitation.

So they didn’t formally disinvite him, but Fogel obviously made clear that Stein wasn’t welcome. Speaking to the UVM student paper, he warmly singled out the influence of Dawkins: Apart from his own faculty, “I heard from very distinguished members of the scientific community like Richard Dawkins as well.”

Dawkins had sent an sent an email to Fogel, saying he was “dismayed” by the invitation to Stein (though apparently not “deeply dismayed”). He asked among other things, “Was anybody in the Biology Department consulted before you issued an invitation to a notoriously mendacious propagandist for creationism?”

Ben Stein himself was blunt in the Burlington Free Press:

Stein called the university’s response to the furor “chicken sh**, and you can quote me on that.”

“I like Dr. Fogel,” Stein wrote, “and feel sorry he is caught in the meat grinder of political correctness. My heart goes out to him. He’s a great guy trying to do his best in difficult circumstances.”

Eight years later, at the center of the row it’s a different university community and a different set of “highly controversial” opinions. Other than that, the parallel is perfect. The shoe is now on the other foot, an audience’s “freedom of listening” has been set aside in deference to political correctness, and Dawkins, suddenly in the role of the silenced rather than the silencer, finds that he doesn’t much like it.

A clash of Titans LVII

A clash of Titans LVI